Genetic loci associated with soybean cyst nematode resistance and methods of use

ABSTRACT

Various methods and compositions are provided for identifying and/or selecting soybean plants or soybean germplasm with improved resistance to soybean cyst nematode. In certain embodiments, the method comprises detecting at least one marker locus that is associated with resistance to soybean cyst nematode. In other embodiments, the method further comprises detecting at least one marker profile or haplotype associated with resistance to soybean cyst nematode. In further embodiments, the method comprises crossing a selected soybean plant with a second soybean plant. Further provided are markers, primers, probes and kits useful for identifying and/or selecting soybean plants or soybean germplasm with improved resistance to soybean cyst nematode.

CROSS-REFERENCES TO RELATED APPLICATIONS

This application claims priority to U.S. Provisional Patent ApplicationSer. No. 61/740,526, filed on Dec. 21, 2012, U.S. Provisional PatentApplication Ser. No. 61/660,387, filed on Jun. 15, 2012, and U.S.Provisional Patent Application Ser. No. 61/671,937, filed Jul. 16, 2012,each of which is hereby incorporated herein in its entirety byreference.

FIELD OF THE INVENTION

This invention relates to methods of identifying and/or selectingsoybean plants or germplasm that display improved resistance to SoybeanCyst Nematode.

REFERENCE TO A SEQUENCE LISTING SUBMITTED AS A TEXT FILE VIA EFS-WEB

The official copy of the sequence listing is submitted concurrently withthe specification as a text file via EFS-Web, in compliance with theAmerican Standard Code for Information Interchange (ASCII), with a filename of 429573seqlist.txt, a creation date of Feb. 18, 2013 and a sizeof 39 KB. The sequence listing filed via EFS-Web is part of thespecification and is hereby incorporated in its entirety by referenceherein.

BACKGROUND

Soybeans (Glycine max L. Merr.) are a major cash crop and investmentcommodity in North America and elsewhere. Soybean oil is one of the mostwidely used edible oils, and soybeans are used worldwide both in animalfeed and in human food production. Additionally, soybean utilization isexpanding to industrial, manufacturing, and pharmaceutical applications.

Soybean Cyst Nematode (SCN) is a parasitic pest which has threatenedsoybean production in the U.S. for more than fifty years. Soybean cystnematode resistance is an economically important trait as infection cansubstantially reduce yields. Molecular characterization of soybean cystnematode resistance would have important implications for soybeancultivar improvement.

There remains a need for soybean plants with improved resistance tosoybean cyst nematode and methods for identifying and selecting suchplants.

SUMMARY

Various methods and compositions are provided for identifying and/orselecting soybean plants or soybean germplasm with improved resistanceto soybean cyst nematode. In certain embodiments, the method comprisesdetecting at least one marker locus that is associated with resistanceto soybean cyst nematode. In other embodiments, the method furthercomprises detecting at least one marker profile or haplotype associatedwith resistance to soybean cyst nematode. In further embodiments, themethod comprises crossing a selected soybean plant with a second soybeanplant. Further provided are markers, primers, probes and kits useful foridentifying and/or selecting soybean plants or soybean germplasm withimproved resistance to soybean cyst nematode.

DETAILED DESCRIPTION

Molecular markers have been used to selectively improve soybean cropsthrough the use of marker assisted selection. Any detectable polymorphictrait can be used as a marker so long as it is inherited differentiallyand exhibits linkage disequilibrium with a phenotypic trait of interest.A number of soybean markers have been mapped and linkage groups created,as described in Cregan, P. B., et al., “An Integrated Genetic LinkageMap of the Soybean Genome” (1999) Crop Science 39:1464-90, and morerecently in Choi, et al., “A Soybean Transcript Map: Gene Distribution,Haplotype and Single-Nucleotide Polymorphism Analysis” (2007) Genetics176:685-96. Many soybean markers are publicly available at the USDAaffiliated soybase website (www.soybase.org).

Most plant traits of agronomic importance are polygenic, otherwise knownas quantitative, traits. A quantitative trait is controlled by severalgenes located at various locations, or loci, in the plant's genome. Themultiple genes have a cumulative effect which contributes to thecontinuous range of phenotypes observed in many plant traits. Thesegenes are referred to as quantitative trait loci (QTL). Recombinationfrequency measures the extent to which a molecular marker is linked witha QTL. Lower recombination frequencies, typically measured incentiMorgans (cM), indicate greater linkage between the QTL and themolecular marker. The extent to which two features are linked is oftenreferred to as the genetic distance. The genetic distance is alsotypically related to the physical distance between the marker and theQTL; however, certain biological phenomenon (including recombinational“hot spots”) can affect the relationship between physical distance andgenetic distance. Generally, the usefulness of a molecular marker isdetermined by the genetic and physical distance between the marker andthe selectable trait of interest.

In some cases, multiple closely linked markers, such as SingleNucleotide Polymorphism (SNP) markers, can be found to exist in acertain region of a plant genome encompassing one or more QTL. In suchcases, by determining the allele present at each of those marker loci, ahaplotype for that region of the plant genome can be determined.Further, by determining alleles or haplotypes present at multipleregions of the plant genome related to the same phenotypic trait, amarker profile for that trait can be determined. Such haplotype andmarker profile information can be useful in identifying and selectingplants with certain desired traits.

Before describing the present invention in detail, it is to beunderstood that this invention is not limited to particular embodiments,which can, of course, vary. It is also to be understood that theterminology used herein is for the purpose of describing particularembodiments only, and is not intended to be limiting.

Certain definitions used in the specification and claims are providedbelow. In order to provide a clear and consistent understanding of thespecification and claims, including the scope to be given such terms,the following definitions are provided:

As used in this specification and the appended claims, terms in thesingular and the singular forms “a,” “an,” and “the,” for example,include plural referents unless the content clearly dictates otherwise.Thus, for example, reference to “plant,” “the plant,” or “a plant” alsoincludes a plurality of plants; also, depending on the context, use ofthe term “plant” can also include genetically similar or identicalprogeny of that plant; use of the term “a nucleic acid” optionallyincludes, as a practical matter, many copies of that nucleic acidmolecule; similarly, the term “probe” optionally (and typically)encompasses many similar or identical probe molecules.

Additionally, as used herein, “comprising” is to be interpreted asspecifying the presence of the stated features, integers, steps, orcomponents as referred to, but does not preclude the presence oraddition of one or more features, integers, steps, or components, orgroups thereof. Thus, for example, a kit comprising one pair ofoligonucleotide primers may have two or more pairs of oligonucleotideprimers. Additionally, the term “comprising” is intended to includeexamples encompassed by the terms “consisting essentially of” and“consisting of:” Similarly, the term “consisting essentially of” isintended to include examples encompassed by the term “consisting of:”

“Agronomics,” “agronomic traits,” and “agronomic performance” refer tothe traits (and underlying genetic elements) of a given plant varietythat contribute to yield over the course of a growing season. Individualagronomic traits include emergence vigor, vegetative vigor, stresstolerance, disease resistance or tolerance, insect resistance ortolerance, herbicide resistance, branching, flowering, seed set, seedsize, seed density, standability, threshability, and the like.

“Allele” means any of one or more alternative forms of a geneticsequence. In a diploid cell or organism, the two alleles of a givensequence typically occupy corresponding loci on a pair of homologouschromosomes. With regard to a SNP marker, allele refers to the specificnucleotide base present at that SNP locus in that individual plant.

The term “amplifying” in the context of nucleic acid amplification isany process whereby additional copies of a selected nucleic acid (or atranscribed form thereof) are produced. An “amplicon” is an amplifiednucleic acid, e.g., a nucleic acid that is produced by amplifying atemplate nucleic acid by any available amplification.

An “ancestral line” is a parent line used as a source of genes, e.g.,for the development of elite lines.

An “ancestral population” is a group of ancestors that have contributedthe bulk of the genetic variation that was used to develop elite lines.

“Backcrossing” is a process in which a breeder crosses a progeny varietyback to one of the parental genotypes one or more times.

The term “chromosome segment” designates a contiguous linear span ofgenomic DNA that resides in planta on a single chromosome. “Chromosomeinterval” refers to a chromosome segment defined by specific flankingmarker loci.

“Cultivar” and “variety” are used synonymously and mean a group ofplants within a species (e.g., Glycine max) that share certain genetictraits that separate them from other possible varieties within thatspecies. Soybean cultivars are inbred lines produced after severalgenerations of self-pollinations. Individuals within a soybean cultivarare homogeneous, nearly genetically identical, with most loci in thehomozygous state.

An “elite line” is an agronomically superior line that has resulted frommany cycles of breeding and selection for superior agronomicperformance. Numerous elite lines are available and known to those ofskill in the art of soybean breeding.

An “elite population” is an assortment of elite individuals or linesthat can be used to represent the state of the art in terms ofagronomically superior genotypes of a given crop species, such assoybean.

An “exotic soybean strain” or an “exotic soybean germplasm” is a strainor germplasm derived from a soybean not belonging to an available elitesoybean line or strain of germplasm. In the context of a cross betweentwo soybean plants or strains of germplasm, an exotic germplasm is notclosely related by descent to the elite germplasm with which it iscrossed. Most commonly, the exotic germplasm is not derived from anyknown elite line of soybean, but rather is selected to introduce novelgenetic elements (typically novel alleles) into a breeding program.

A “genetic map” is a description of genetic association or linkagerelationships among loci on one or more chromosomes (or linkage groups)within a given species, generally depicted in a diagrammatic or tabularform.

“Genotype” is a description of the allelic state at one or more loci.

“Germplasm” means the genetic material that comprises the physicalfoundation of the hereditary qualities of an organism. As used herein,germplasm includes seeds and living tissue from which new plants may begrown; or, another plant part, such as leaf, stem, pollen, or cells,that may be cultured into a whole plant. Germplasm resources providesources of genetic traits used by plant breeders to improve commercialcultivars.

An individual is “homozygous” if the individual has only one type ofallele at a given locus (e.g., a diploid individual has a copy of thesame allele at a locus for each of two homologous chromosomes). Anindividual is “heterozygous” if more than one allele type is present ata given locus (e.g., a diploid individual with one copy each of twodifferent alleles). The term “homogeneity” indicates that members of agroup have the same genotype at one or more specific loci. In contrast,the term “heterogeneity” is used to indicate that individuals within thegroup differ in genotype at one or more specific loci.

“Introgression” means the entry or introduction of a gene, QTL,haplotype, marker profile, trait, or trait locus from the genome of oneplant into the genome of another plant.

The terms “label” or “detectable label” refer to a molecule capable ofdetection. A detectable label can also include a combination of areporter and a quencher, such as are employed in FRET probes or TaqMan™probes. The term “reporter” refers to a substance or a portion thereofwhich is capable of exhibiting a detectable signal, which signal can besuppressed by a quencher. The detectable signal of the reporter is,e.g., fluorescence in the detectable range. The term “quencher” refersto a substance or portion thereof which is capable of suppressing,reducing, inhibiting, etc., the detectable signal produced by thereporter. As used herein, the terms “quenching” and “fluorescence energytransfer” refer to the process whereby, when a reporter and a quencherare in close proximity, and the reporter is excited by an energy source,a substantial portion of the energy of the excited state non-radiativelytransfers to the quencher where it either dissipates non-radiatively oris emitted at a different emission wavelength than that of the reporter.

A “line” or “strain” is a group of individuals of identical parentagethat are generally inbred to some degree and that are generallyhomozygous and homogeneous at most loci (isogenic or near isogenic). A“subline” refers to an inbred subset of descendants that are geneticallydistinct from other similarly inbred subsets descended from the sameprogenitor. Traditionally, a subline has been derived by inbreeding theseed from an individual soybean plant selected at the F3 to F5generation until the residual segregating loci are “fixed” or homozygousacross most or all loci. Commercial soybean varieties (or lines) aretypically produced by aggregating (“bulking”) the self-pollinatedprogeny of a single F3 to F5 plant from a controlled cross between 2genetically different parents. While the variety typically appearsuniform, the self-pollinating variety derived from the selected planteventually (e.g., F8) becomes a mixture of homozygous plants that canvary in genotype at any locus that was heterozygous in the originallyselected F3 to F5 plant. Marker-based sublines that differ from eachother based on qualitative polymorphism at the DNA level at one or morespecific marker loci are derived by genotyping a sample of seed derivedfrom individual self-pollinated progeny derived from a selected F3-F5plant. The seed sample can be genotyped directly as seed, or as planttissue grown from such a seed sample. Optionally, seed sharing a commongenotype at the specified locus (or loci) are bulked providing a sublinethat is genetically homogenous at identified loci important for a traitof interest (e.g., yield, tolerance, etc.).

“Linkage” refers to the tendency for alleles to segregate together moreoften than expected by chance if their transmission was independent.Typically, linkage refers to alleles on the same chromosome. Geneticrecombination occurs with an assumed random frequency over the entiregenome. Genetic maps are constructed by measuring the frequency ofrecombination between pairs of traits or markers, the lower thefrequency of recombination, and the greater the degree of linkage.

“Linkage disequilibrium” is a non-random association of alleles at twoor more loci and can occur between unlinked markers. It is based onallele frequencies within a population and is influenced by but notdependent on linkage.

“Linkage group” (LG) refers to traits or markers that generallyco-segregate. A linkage group generally corresponds to a chromosomalregion containing genetic material that encodes the traits or markers.

“Locus” is a defined segment of DNA.

A “map location” or “map position” is an assigned location on a geneticmap relative to linked genetic markers where a specified marker can befound within a given species. Map positions are generally provided incentimorgans (cM)), unless otherwise indicated, genetic positionsprovided are based on the Glycine max consensus map v 4.0 as provided byHyten et al. (2010) Crop Sci 50:960-968. A “physical position” or“physical location” or “physical map location” is the position,typically in nucleotides bases, of a particular nucleotide, such as aSNP nucleotide, on a chromosome. Unless otherwise indicated, thephysical position within the soybean genome provided is based on theGlyma 1.0 genome sequence described in Schmutz et al. (2010) Nature463:178-183, available from the Phytozome website(phytozome-dot-net/soybean).

“Mapping” is the process of defining the association and relationshipsof loci through the use of genetic markers, populations segregating forthe markers, and standard genetic principles of recombination frequency.

“Marker” or “molecular marker” or “marker locus” is a term used todenote a nucleic acid or amino acid sequence that is sufficiently uniqueto characterize a specific locus on the genome. Any detectablepolymorphic trait can be used as a marker so long as it is inheriteddifferentially and exhibits linkage disequilibrium with a phenotypictrait of interest.

“Marker assisted selection” refers to the process of selecting a desiredtrait or traits in a plant or plants by detecting one or more nucleicacids from the plant, where the nucleic acid is linked to the desiredtrait, and then selecting the plant or germplasm possessing those one ormore nucleic acids.

“Haplotype” refers to a combination of particular alleles present withina particular plant's genome at two or more linked marker loci, forinstance at two or more loci on a particular linkage group. Forinstance, in one example, two specific marker loci on LG-O are used todefine a haplotype for a particular plant. In still further examples, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or morelinked marker loci are used to define a haplotype for a particularplant.

As used herein, a “marker profile” means a combination of particularalleles present within a particular plant's genome at two or more markerloci which are not linked, for instance two or more loci on two or moredifferent linkage groups or two or more chromosomes. For instance, inone example, a particular combination of marker loci or a particularcombination of haplotypes define the marker profile of a particularplant.

The term “plant” includes reference to an immature or mature wholeplant, including a plant from which seed or grain or anthers have beenremoved. Seed or embryo that will produce the plant is also consideredto be the plant.

“Plant parts” means any portion or piece of a plant, including leaves,stems, buds, roots, root tips, anthers, seed, grain, embryo, pollen,ovules, flowers, cotyledons, hypocotyls, pods, flowers, shoots, stalks,tissues, tissue cultures, cells and the like.

“Polymorphism” means a change or difference between two related nucleicacids. A “nucleotide polymorphism” refers to a nucleotide that isdifferent in one sequence when compared to a related sequence when thetwo nucleic acids are aligned for maximal correspondence.

“Polynucleotide,” “polynucleotide sequence,” “nucleic acid,” “nucleicacid molecule,” “nucleic acid sequence,” “nucleic acid fragment,” and“oligonucleotide” are used interchangeably herein to indicate a polymerof nucleotides that is single- or multi-stranded, that optionallycontains synthetic, non-natural, or altered RNA or DNA nucleotide bases.A DNA polynucleotide may be comprised of one or more strands of cDNA,genomic DNA, synthetic DNA, or mixtures thereof.

“Primer” refers to an oligonucleotide which is capable of acting as apoint of initiation of nucleic acid synthesis or replication along acomplementary strand when placed under conditions in which synthesis ofa complementary strand is catalyzed by a polymerase. Typically, primersare about 10 to 30 nucleotides in length, but longer or shortersequences can be employed. Primers may be provided in double-strandedform, though the single-stranded form is more typically used. A primercan further contain a detectable label, for example a 5′ end label.

“Probe” refers to an oligonucleotide that is complementary (though notnecessarily fully complementary) to a polynucleotide of interest andforms a duplexed structure by hybridization with at least one strand ofthe polynucleotide of interest. Typically, probes are oligonucleotidesfrom 10 to 50 nucleotides in length, but longer or shorter sequences canbe employed. A probe can further contain a detectable label.

“Quantitative trait loci” or “QTL” refer to the genetic elementscontrolling a quantitative trait.

“Recombination frequency” is the frequency of a crossing over event(recombination) between two genetic loci. Recombination frequency can beobserved by following the segregation of markers and/or traits duringmeiosis.

“Resistance and “improved resistance” are used interchangeably hereinand refer to any type of increase in resistance or resistance to, or anytype of decrease in susceptibility. A “resistant plant” or “resistantplant variety” need not possess absolute or complete resistance.Instead, a “resistant plant,” “resistant plant variety,” or a plant orplant variety with “improved resistance” will have a level of resistanceor tolerance which is higher than that of a comparable susceptible plantor variety.

“Self-crossing” or “self-pollination” or “selfing” is a process throughwhich a breeder crosses a plant with itself; for example, a secondgeneration hybrid F2 with itself to yield progeny designated F2:3.

“SNP” or “single nucleotide polymorphism” means a sequence variationthat occurs when a single nucleotide (A, T, C, or G) in the genomesequence is altered or variable. “SNP markers” exist when SNPs aremapped to sites on the soybean genome.

The term “yield” refers to the productivity per unit area of aparticular plant product of commercial value. For example, yield ofsoybean is commonly measured in bushels of seed per acre or metric tonsof seed per hectare per season. Yield is affected by both genetic andenvironmental factors.

As used herein, an “isolated” or “purified” polynucleotide orpolypeptide, or biologically active portion thereof, is substantially oressentially free from components that normally accompany or interactwith the polynucleotide or polypeptide as found in its naturallyoccurring environment. Typically, an “isolated” polynucleotide is freeof sequences (optimally protein encoding sequences) that naturally flankthe polynucleotide (i.e., sequences located at the 5′ and 3′ ends of thepolynucleotide) in the genomic DNA of the organism from which thepolynucleotide is derived. For example, the isolated polynucleotide cancontain less than about 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb, or 0.1 kbof nucleotide sequence that naturally flank the polynucleotide ingenomic DNA of the cell from which the polynucleotide is derived. Apolypeptide that is substantially free of cellular material includespreparations of polypeptides having less than about 30%, 20%, 10%, 5%,or 1% (by dry weight) of contaminating protein, culture media or otherchemical components.

Standard recombinant DNA and molecular cloning techniques used hereinare well known in the art and are described more fully in Sambrook, J.,Fritsch, E. F. and Maniatis, T. Molecular Cloning: A Laboratory Manual;Cold Spring Harbor Laboratory Press: Cold Spring Harbor, 1989(hereinafter “Sambrook”).

Methods are provided for identifying and/or selecting a soybean plant orsoybean germplasm that displays improved resistance to soybean cystnematode. The method comprises detecting in the soybean plant orgermplasm, or a part thereof, at least one marker locus associated withresistance to soybean cyst nematode. Also provided are isolatedpolynucleotides and kits for use in identifying and/or detecting asoybean plant or soybean germplasm that displays improved resistance tosoybean cyst nematode, and soybean plants, cells, and/or seedscomprising at least one marker locus conferring improved resistance tosoybean cyst nematode.

Provided herein are marker loci associated with soybean cyst nematoderesistance that have been identified and mapped to genomic loci onlinkage group G. These findings have important implications for soybeanproduction, as identifying markers that can be used for selection ofsoybean cyst nematode resistance will greatly expedite the developmentof soybean cyst nematode resistance into elite cultivars.

Marker loci, haplotypes and marker profiles associated with resistanceto soybean cyst nematode are provided. Further provided are genomic locithat are associated with soybean resistance to soybean cyst nematode.

In certain embodiments, soybean plants or germplasm are identified thathave at least one favorable allele, marker locus, haplotype or markerprofile that positively correlates with resistance or improvedresistance to soybean cyst nematode. However, in other embodiments, itis useful for exclusionary purposes during breeding to identify alleles,marker loci, haplotypes, or marker profiles that negatively correlatewith resistance, for example, to eliminate such plants or germplasm fromsubsequent rounds of breeding.

In one embodiment, marker loci useful for identifying a first soybeanplant or first soybean germplasm that displays improved resistance tosoybean cyst nematode comprises a marker locus comprising one or more of(a) the at least one marker locus comprises 508271-1-Q2 or a markerclosely linked thereto on linkage group G; (b) the at least one markerlocus comprises P7659A-2 or a marker closely linked thereto on linkagegroup G; (c) the at least one marker locus comprises S08051-1-Q1 or amarker closely linked thereto on linkage group G; (d) the at least onemarker locus comprises S07158-1-Q1 or a marker closely linked thereto onlinkage group G; (e) the at least one marker locus comprises S07159-1-Q1or a marker closely linked thereto on linkage group G; (f) the at leastone marker locus comprises S06818-3-Q2 or a marker closely linkedthereto on linkage group G; (g) the at least one marker locus comprisesS06820-1-Q3 or a marker closely linked thereto on linkage group G; (h)the at least one marker locus comprises S06821-1-Q2 or a marker closelylinked thereto on linkage group G; (i) the at least one marker locuscomprises S16001-001-Q001 or a marker closely linked thereto on linkagegroup G; (j) the at least one marker locus is between about markerSatt309 and BARC-012285-01798 on linkage group G; (k) the at least onemarker locus is between about marker BARC-015371-01813 andBARCSOYSSR_(—)18_(—)0093 on linkage group G; (l) the at least one markerlocus is between about marker BARC-030055-06792 and BARC-025777-05064 onlinkage group G; (m) the at least one marker locus is between aboutmarker BARC-015371-01813 and BARCSOYSSR_(—)18_(—)0093 on linkage groupG; (n) the at least one marker locus is between about markerBARC-015371-01813 and BARCSOYSSR_(—)18_(—)0093 on linkage group G; or(o) the at least one marker locus comprises at least one of Gm18:926125;Gm18:1138152; Gm18:1517146; Gm18:1518206; Gm18:1520624; Gm18:1520675;Gm18:1520743; Gm18:1524498; Gm18:1548716; Gm18:1550153; Gm18:1550231;Gm18:1552799; Gm18:1554392; Gm18:1554570; Gm18:1554604; Gm18:1554689;Gm18:1555210; Gm18:1560043; Gm18:1560088; Gm18:1560390; Gm18:1560442;Gm18:1560784; Gm18:1561009; Gm18:1561190; Gm18:1561429; Gm18:1561725;Gm18:1562884; Gm18:1563153; Gm18:1564092; Gm18:1565225; Gm18:1565646;Gm18:1566882; Gm18:1567685; Gm18:1567843; Gm18:1568490; Gm18:1568999;Gm18:1569035; Gm18:1569146; Gm18:1570660; Gm18:1572368; Gm18:1577559;Gm18:1578727; Gm18:1579201; Gm18:1579270; Gm18:1579707; Gm18:1579708;Gm18:1581688; Gm18:1583772; Gm18:1584054; Gm18:1584659; Gm18:1589032;Gm18:1595321; Gm18:1598101; Gm18:1599717; Gm18:1599752; Gm18:1599841;Gm18:1600011; Gm18:1600033; Gm18:1600179; Gm18:1601192; Gm18:1601614;Gm18:1602244; Gm18:1603722; Gm18:1604031; Gm18:1605443; Gm18:1606442;Gm18:1606566; Gm18:1606647; Gm18:1609397; Gm18:1610935; Gm18:1612466;Gm18:1612553; Gm18:1614300; Gm18:1614960 Gm18:1618118; Gm18:1626263;Gm18:1626278; Gm18:1627202; Gm18:1627204; Gm18:1629930; Gm18:1634611;Gm18:1643225; Gm18:1653887; Gm18:1654681; Gm18:1654687; Gm18:1657025;Gm18:1680507; Gm18:1700832; Gm18:1700885; Gm18:1701854; Gm18:1702482;Gm18:1702563; Gm18:1702741; Gm18:1703321; Gm18:1706708; Gm18:1706842;Gm18:1707082; Gm18:1707115; Gm18:1707377; Gm18:1708549; Gm18:1717352;Gm18:1721829; Gm18:1723649; Gm18:1723650; Gm18:1724082; Gm18:172553;Gm18:1725630; Gm18:1725815; Gm18:1725932; Gm18:1725991; Gm18:1726068;Gm18:1727330; Gm18:1727343; Gm18:1727903; Gm18:1728146; Gm18:1728824;Gm18:1729347; Gm18:1729673; Gm18:1729866; Gm18:1730855; Gm18:1731068;Gm18:1731184; Gm18:1731725; Gm18:1731938; Gm18:1734691; Gm18:1735510;Gm18:1740118; Gm18:1747766; Gm18:1751156; Gm18:1752808; Gm18:1754310;Gm18:1754895; Gm18:1759167; Gm18:1759307; Gm18:1761263; Gm18:1762686;Gm18:1763519; Gm18:1768783; Gm18:1768805; Gm18:1769619; Gm18:1773903;Gm18:1773911; Gm18:1778021; Gm18:1783028; Gm18:1783194; Gm18:1783357;Gm18:1785320; Gm18:1787549; Gm18:1789215; Gm18:1789352; Gm18:1789553;Gm18:1789934; Gm18:1805509; Gm18:1859739; Gm18:1863987; Gm18:1864738;Gm18:1877951; Gm18:1881755; Gm18:1607524; Gm18:1888247; Gm18:1845911;Gm18:1846008; Gm18:1565826; or Gm18:1918014; or a marker closely linkedthereto on linkage group G.

Non-limiting examples of marker loci located within, linked to, orclosely linked to these genomic loci are provided in Table 1A.

TABLE 1 Marker Positions For Marker Loci Associated With Resistance toSoybean Cyst Nematode. Linkage GmConsensus % var Marker ID groupFlanking public marker 4.0 (cM) Phys Map Allele (R/S) Analysis,Statistic Xplnd Source S08271-1-Q2 G ‘Satt309 (10.1); ‘BARC- 10.161749394 A/T Association Mapping, p- PI88788 (P10355B-1) 012285-01798(11.0) value 0.0000000000012402, chi square 50.422 P7659A-2 G‘BARC-015371-01813 9.27 1580305 T/C (8.63); ‘BARCSOYSSR_18_0093 (9.44)S08051-1-Q1 G ‘BARC-015371-01813 9.26 1579707 GT/TC Association Mapping,p- Peking, (P7659A-1) (8.63); and value 2.3816E−21, chi PI437654‘BARCSOYSSR_18_0093 1579708 square 90 (9.44) S07158-1-Q1 G‘BARC-030055-06792 12.34 2098742 TG/GT PI437654, (P5219A-1) (12.15);‘BARC-025777- and PI88788, 05064 (12.92) 2098741 Peking S07159-1-Q1 G‘BARC-030055-06792 12.33 2095977 T/A PI437654 (P5219A-2) (12.15);‘BARC-025777- 05064 (12.92) S06818-3-Q2 G ‘BARC-015371-01813 9.231573060 C/G Association mapping, p- (8.63); value 1.2876E−37, chi‘BARCSOYSSR_18_0093 square 164.32 (9.44) S06820-1-Q3 G‘BARC-015371-01813 9.22 1571774 G/A (8.63); ‘BARCSOYSSR_18_0093 (9.44)S06821-1-Q2 G ‘BARC-015371-01813 9.19 1563924 T/G (8.63);‘BARCSOYSSR_18_0093 (9.44) S16001-001- G ‘BARC-015371-01813 9.38 1607524C/A Association Mapping, p- PI88788 Q001 (8.63); value 2.0885E−45, chi‘BARCSOYSSR_18_0093 square 200 (9.44) Gm18: 926125 G  926125 See table13 Gm18: 1138152 G 1138152 See table 13 Gm18: 1517146 G 1517146 Seetable 13 Gm18: 1518206 G 1518206 See table 13 Gm18: 1520624 G 1520624See table 13 Gm18: 1520675 G 1520675 See table 13 Gm18: 1520743 G1520743 See table 13 Gm18: 1524498 G 1524498 See table 13 Gm18: 1548716G 1548716 See table 13 Gm18: 1550153 G 1550153 See table 13 Gm18:1550231 G 1550231 See table 13 Gm18: 1552799 G 1552799 See table 13Gm18: 1554392 G 1554392 See table 13 Gm18: 1554570 G 1554570 See table13 Gm18: 1554604 G 1554604 See table 13 Gm18: 1554689 G 1554689 Seetable 13 Gm18: 1555210 G 1555210 See table 13 Gm18: 1560043 G 1560043See table 13 Gm18: 1560088 G 1560088 See table 13 Gm18: 1560390 G1560390 See table 13 Gm18: 1560442 G 1560442 See table 13 Gm18: 1560784G 1560784 See table 13 Gm18: 1561009 G 1561009 See table 13 Gm18:1561190 G 1561190 See table 13 Gm18: 1561429 G 1561429 See table 13Gm18: 1561725 G 1561725 See table 13 Gm18: 1562884 G 1562884 See table13 Gm18: 1563153 G 1563153 See table 13 Gm18: 1564092 G 1564092 Seetable 13 Gm18: 1565225 G 1565225 See table 13 Gm18: 1565646 G 1565646See table 13 Gm18: 1566882 G 1566882 See table 13 Gm18: 1567685 G1567685 See table 13 Gm18: 1567843 G 1567843 See table 13 Gm18: 1568490G 1568490 See table 13 Gm18: 1568999 G 1568999 See table 13 Gm18:1569035 G 1569035 See table 13 Gm18: 1569146 G 1569146 See table 13Gm18: 1570660 G 1570660 See table 13 Gm18: 1572368 G 1572368 See table13 Gm18: 1577559 G 1577559 See table 13 Gm18: 1578727 G 1578727 Seetable 13 Gm18: 1579201 G 1579201 See table 13 Gm18: 1579270 G 1579270See table 13 Gm18: 1579707 G 1579707 See table 13 Gm18: 1579708 G1579708 See table 13 Gm18: 1581688 G 1581688 See table 13 Gm18: 1583772G 1583772 See table 13 Gm18: 1584054 G 1584054 See table 13 Gm18:1584659 G 1584659 See table 13 Gm18: 1589032 G 1589032 See table 13Gm18: 1595321 G 1595321 See table 13 Gm18: 1598101 G 1598101 See table13 Gm18: 1599717 G 1599717 See table 13 Gm18: 1599752 G 1599752 Seetable 13 Gm18: 1599841 G 1599841 See table 13 Gm18: 1600011 G 1600011See table 13 Gm18: 1600033 G 1600033 See table 13 Gm18: 1600179 G1600179 See table 13 Gm18: 1601192 G 1601192 See table 13 Gm18: 1601614G 1601614 See table 13 Gm18: 1602244 G 1602244 See table 13 Gm18:1603722 G 1603722 See table 13 Gm18: 1604031 G 1604031 See table 13Gm18: 1605443 G 1605443 See table 13 Gm18: 1606442 G 1606442 See table13 Gm18: 1606566 G 1606566 See table 13 Gm18: 1606647 G 1606647 Seetable 13 Gm18: 1609397 G 1609397 See table 13 Gm18: 1610935 G 1610935See table 13 Gm18: 1612466 G 1612466 See table 13 Gm18: 1612553 G1612553 See table 13 Gm18: 1614300 G 1614300 See table 13 Gm18: 1614960G 1614960 See table 13 Gm18: 1618118 G 1618118 See table 13 Gm18:1626263 G 1626263 See table 13 Gm18: 1626278 G 1626278 See table 13Gm18: 1627202 G 1627202 See table 13 Gm18: 1627204 G 1627204 See table13 Gm18: 1629930 G 1629930 See table 13 Gm18: 1634611 G 1634611 Seetable 13 Gm18: 1643225 G 1643225 See table 13 Gm18: 1653887 G 1653887See table 13 Gm18: 1654681 G 1654681 See table 13 Gm18: 1654687 G1654687 See table 13 Gm18: 1657025 G 1657025 See table 13 Gm18: 1680507G 1680507 See table 13 Gm18: 1700832 G 1700832 See table 13 Gm18:1700885 G 1700885 See table 13 Gm18: 1701854 G 1701854 See table 13Gm18: 1702482 G 1702482 See table 13 Gm18: 1702563 G 1702563 See table13 Gm18: 1702741 G 1702741 See table 13 Gm18: 1703321 G 1703321 Seetable 13 Gm18: 1706708 G 1706708 See table 13 Gm18: 1706842 G 1706842See table 13 Gm18: 1707082 G 1707082 See table 13 Gm18: 1707115 G1707115 See table 13 Gm18: 1707377 G 1707377 See table 13 Gm18: 1708549G 1708549 See table 13 Gm18: 1717352 G 1717352 See table 13 Gm18:1721829 G 1721829 See table 13 Gm18: 1723649 G 1723649 See table 13Gm18: 1723650 G 1723650 See table 13 Gm18: 1724082 G 1724082 See table13 Gm18: 1725538 G 1725538 See table 13 Gm18: 1725630 G 1725630 Seetable 13 Gm18: 1725815 G 1725815 See table 13 Gm18: 1725932 G 1725932See table 13 Gm18: 1725991 G 1725991 See table 13 Gm18: 1726068 G1726068 See table 13 Gm18: 1727330 G 1727330 See table 13 Gm18: 1727343G 1727343 See table 13 Gm18: 1727903 G 1727903 See table 13 Gm18:1728146 G 1728146 See table 13 Gm18: 1728824 G 1728824 See table 13Gm18: 1729347 G 1729347 See table 13 Gm18: 1729673 G 1729673 See table13 Gm18: 1729866 G 1729866 See table 13 Gm18: 1730855 G 1730855 Seetable 13 Gm18: 1731068 G 1731068 See table 13 Gm18: 1731184 G 1731184See table 13 Gm18: 1731725 G 1731725 See table 13 Gm18: 1731938 G1731938 See table 13 Gm18: 1734691 G 1734691 See table 13 Gm18: 1735510G 1735510 See table 13 Gm18: 1740118 G 1740118 See table 13 Gm18:1747766 G 1747766 See table 13 Gm18: 1751156 G 1751156 See table 13Gm18: 1752808 G 1752808 See table 13 Gm18: 1754310 G 1754310 See table13 Gm18: 1754895 G 1754895 See table 13 Gm18: 1759167 G 1759167 Seetable 13 Gm18: 1759307 G 1759307 See table 13 Gm18: 1761263 G 1761263See table 13 Gm18: 1762686 G 1762686 See table 13 Gm18: 1763519 G1763519 See table 13 Gm18: 1768783 G 1768783 See table 13 Gm18: 1768805G 1768805 See table 13 Gm18: 1769619 G 1769619 See table 13 Gm18:1773903 G 1773903 See table 13 Gm18: 1773911 G 1773911 See table 13Gm18: 1778021 G 1778021 See table 13 Gm18: 1783028 G 1783028 See table13 Gm18: 1783194 G 1783194 See table 13 Gm18: 1783357 G 1783357 Seetable 13 Gm18: 1785320 G 1785320 See table 13 Gm18: 1787549 G 1787549See table 13 Gm18: 1789215 G 1789215 See table 13 Gm18: 1789352 G1789352 See table 13 Gm18: 1789553 G 1789553 See table 13 Gm18: 1789934G 1789934 See table 13 Gm18: 1805509 G 1805509 See table 13 Gm18:1859739 G 1859739 See table 13 Gm18: 1863987 G 1863987 See table 13Gm18: 1864738 G 1864738 See table 13 Gm18: 1877951 G 1877951 See table13 Gm18: 1881755 G 1881755 See table 13 Gm18: 1607524 G 1607524 Seetable 15 Gm18: 1888247 G 1845911 See table 15 Gm18: 1845911 G 1845911See table 15 Gm18: 1846008 G 1846008 See table 15 Gm18: 1565826 G1565826 See table 15 Gm18: 1918014 G 1918014 See table 15

TABLE 1A Non-limiting examples of markers closely linked to variousmarkers set forth in Table 1. Linkage GmConsensus Marker ID group 4.0(cM) Phys Map BARC-020027-04405 G_(18) 0.00 181,064 BARC-052957-11678G_(18) 0.00 187,414 BARC-064665-18774 G_(18) 0.11 224,648BARC-043197-08552 G_(18) 0.92 305,200 BARC-060195-16470 G_(18) 1.64470,340 BARC-018387-03171 G_(18) 7.01 488,479 BARC-022431-04323 G_(18)7.43 734,360 BARC-020839-03962 G_(18) 8.12 981,378 BARC-900558-00952G_(18) 8.12 999,063 BARC-049013-10791 G_(18) 8.39 1,277,303BARC-015371-01813 G_(18) 8.63 1,431,827 S06821-1 G_(18) 9.19 1,563,924S06820-1 G_(18) 9.22 1,571,774 S06818-3 G_(18) 9.23 1,573,060 S08051-1G_(18) 9.26 1,579,708 S16001-001 G_(18) 9.38 1,607,524BARCSOYSSR_18_0093 G_(18) 9.44 1,621,261 Sat_210 G_(18) 9.44 1,621,261BARC-048245-10515 G_(18) 9.94 1,718,204 BARC-G00219-00248 G_(18) 9.961,726,610 BARCSOYSSR_18_0102 G_(18) 10.10 1,736,324 Satt309 G_(18) 10.101,736,324 S08271-1 G_(18) 10.16 1,749,394 BARC-012285-01798 G_(18) 11.011,945,192 BARC-010917-01706 G_(18) 11.09 1,955,436 BARC-012289-01799G_(18) 11.12 1,957,590 BARC-028299-05817 G_(18) 11.86 1,958,726BARC-061523-17249 G_(18) 12.10 1,979,049 BARC-030055-06792 G_(18) 12.152,033,662 S07159-1 G_(18) 12.33 2,095,977 S07158-1 G_(18) 12.342,098,742 BARC-025777-05064 G_(18) 12.92 2,296,490 BARCSOYSSR_18_0142G_(18) 13.98 2,409,497 Sat_141 G_(18) 13.98 2,409,497 BARC-004952-00267G_(18) 14.20 2,664,887 BARCSOYSSR_18_0158 G_(18) 14.70 2,665,098 Satt610G_(18) 14.70 2,665,098 BARC-047665-10370 G_(18) 15.97 2,833,064BARC-047787-10396 G_(18) 16.14 2,853,047 BARCSOYSSR_18_0177 G_(18) 17.193,162,740 Satt570 G_(18) 17.19 3,162,740 BARC-014395-01348 G_(18) 19.483,448,063 BARCSOYSSR_18_0195 G_(18) 20.57 3,603,119 AW734137 G_(18)20.57 3,603,119 BARC-003432-00279 G_(18) 21.48 3,643,846BARCSOYSSR_18_0250 G_(18) 22.22 4,692,375 Satt217 G_(18) 22.22 4,692,375BARCSOYSSR_18_0257 G_(18) 24.96 4,800,515 Satt235 G_(18) 24.96 4,800,515BARCSOYSSR_18_0295 G_(18) 29.20 5,330,646 Sat_315 G_(18) 29.20 5,330,646BARCSOYSSR_18_0305 G_(18) 31.02 5,470,147 Sat_290 G_(18) 31.02 5,470,147BARCSOYSSR_18_0316 G_(18) 32.88 5,675,379 Sat_131 G_(18) 32.88 5,675,379BARCSOYSSR_18_0324 G_(18) 35.43 5,890,285 Satt324 G_(18) 35.43 5,890,285BARCSOYSSR_18_0348 G_(18) 36.97 6,169,586 Sat_403 G_(18) 36.97 6,169,586BARC-040265-07700 G_(18) 39.86 7,275,891 BARC-901121-00988 G_(18) 40.418,415,710 BARC-063985-18522 G_(18) 40.41 8,791,883 BARC-039993-07626G_(18) 40.81 9,012,214 BARCSOYSSR_18_0550 G_(18) 43.03 11,400,889Sat_308 G_(18) 43.03 11,400,889 BARC-053419-11845 G_(18) 44.9912,638,074 BARC-056521-14449 G_(18) 47.51 14,167,067 BARC-059783-16090G_(18) 47.51 14,285,415 BARC-054849-12183 G_(18) 47.51 14,335,308BARC-049885-09225 G_(18) 48.21 14,570,865 BARC-064283-18606 G_(18) 48.2114,893,358 BARC-017647-02654 G_(18) 48.33 15,242,485 BARC-059485-15839G_(18) 48.95 15,676,568 BARC-040485-07753 G_(18) 48.95 15,723,524BARC-018333-03580 G_(18) 50.04 16,483,354 BARC-018333-03581 G_(18) 50.2416,483,354 BARC-019465-03616 G_(18) 50.88 16,505,062 BARC-013677-01228G_(18) 52.04 16,668,537 BARC-061001-16998 G_(18) 52.04 16,797,216BARC-047404-12924 G_(18) 52.04 17,550,827 BARC-046912-12782 G_(18) 52.0417,553,931 BARC-046994-12826 G_(18) 52.04 17,575,698 BARC-046874-12778G_(18) 52.04 17,592,240 BARC-046872-12776 G_(18) 52.04 17,600,728BARC-046920-12786 G_(18) 52.04 17,603,029 BARC-046930-12795 G_(18) 52.0417,611,727 BARC-046926-12788 G_(18) 52.04 17,626,176 BARC-046922-12787G_(18) 52.04 17,630,432 BARC-057295-14678 G_(18) 52.04 17,781,283BARC-020159-04488 G_(18) 52.04 17,925,069 BARC-060837-16930 G_(18) 52.0418,410,099 BARC-058413-15279 G_(18) 53.38 20,526,141 BARC-060825-16919G_(18) 54.45 21,121,950 BARC-047150-12874 G_(18) 54.45 21,364,220BARC-047112-12860 G_(18) 54.45 21,365,038 BARC-047096-12838 G_(18) 54.4521,384,584 BARC-063705-18440 G_(18) 54.45 21,701,030 BARC-055557-13432G_(18) 54.45 21,724,083 BARC-062097-17654 G_(18) 54.45 22,120,170BARCSOYSSR_18_0845 G_(18) 54.97 22,150,302 Satt303 G_(18) 54.9722,150,302 BARC-060189-16468 G_(18) 55.60 22,483,339 BARC-047504-12947G_(18) 55.60 22,535,676 BARC-061785-17386 G_(18) 55.60 22,585,948BARC-047502-12946 G_(18) 55.60 22,588,708 BARC-047102-12842 G_(18) 55.6022,603,647 BARC-055855-13794 G_(18) 55.60 23,123,288 BARC-061111-17050G_(18) 55.60 24,129,395 BARC-058369-15257 G_(18) 55.60 27,610,750BARC-060613-16749 G_(18) 55.60 27,931,082 BARC-013825-01251 G_(18) 55.6030,313,907 BARC-061647-17305 G_(18) 55.60 31,080,816 BARC-056139-14122G_(18) 55.60 31,828,672 BARC-059397-15790 G_(18) 55.60 33,110,626BARC-062783-18056 G_(18) 55.60 33,753,070 BARC-030691-06926 G_(18) 55.6034,178,194 BARC-057565-14836 G_(18) 55.60 34,232,818 BARC-056267-14204G_(18) 55.60 36,963,309 BARC-061197-17134 G_(18) 55.60 39,413,323BARC-051485-11122 G_(18) 55.60 39,512,471 BARC-014783-01660 G_(18) 55.6041,560,487 BARC-061717-17358 G_(18) 55.60 41,730,041 BARC-044235-08650G_(18) 55.60 42,206,429 BARC-059239-15686 G_(18) 56.18 43,529,731BARC-056035-13999 G_(18) 56.71 45,468,441 BARC-050493-09699 G_(18) 56.8245,951,229 BARCSOYSSR_18_1146 G_(18) 57.07 46,265,580 Satt533 G_(18)57.07 46,265,580 BARCSOYSSR_18_1210 G_(18) 57.82 48,532,689 Satt504G_(18) 57.82 48,532,689 BARCSOYSSR_18_1348 G_(18) 59.89 52,189,343Sat_185 G_(18) 59.89 52,189,343 BARCSOYSSR_18_1349 G_(18) 59.9052,210,836 Sat_203 G_(18) 59.90 52,210,836 BARCSOYSSR_18_1364 G_(18)60.60 52,465,758 Satt199 G_(18) 60.60 52,465,758 BARCSOYSSR_18_1385G_(18) 60.97 52,746,490 Sat_260 G_(18) 60.97 52,746,490BARCSOYSSR_18_1418 G_(18) 63.44 53,445,942 Satt012 G_(18) 63.4453,445,942 BARC-056635-14538 G_(18) 63.92 53,471,513 BARCSOYSSR_18_1426G_(18) 65.78 53,656,489 Sat_164 G_(18) 65.78 53,656,489BARCSOYSSR_18_1431 G_(18) 66.39 53,769,539 Satt517 G_(18) 66.3953,769,539 BARC-027694-06635 G_(18) 67.91 54,764,508 BARC-050613-09770G_(18) 69.50 54,942,320 BARC-024489-04936 G_(18) 70.62 55,001,002BARC-055139-13077 G_(18) 71.46 55,458,709 BARC-061783-18883 G_(18) 72.0255,506,257 BARC-048761-10703 G_(18) 72.84 56,086,706 BARC-016867-02359G_(18) 73.34 56,429,486 BARC-018441-03188 G_(18) 73.80 56,429,542BARC-052045-11324 G_(18) 75.00 57,071,922 BARC-026013-05225 G_(18) 75.6457,185,832 BARC-015063-02553 G_(18) 76.88 57,353,963 BARC-008223-00022G_(18) 78.05 57,436,269 BARC-032277-08935 G_(18) 79.40 57,462,526BARC-041705-08069 G_(18) 80.96 57,781,784 BARC-032785-09037 G_(18) 80.9657,781,833 BARCSOYSSR_18_1703 G_(18) 85.66 58,093,491 Sct_199 G_(18)85.66 58,093,491 BARCSOYSSR_18_1708 G_(18) 85.98 58,136,286 Satt472G_(18) 85.98 58,136,286 BARC-048095-10484 G_(18) 86.59 58,177,377BARC-038873-07372 G_(18) 87.30 58,438,994 BARCSOYSSR_18_1750 G_(18)89.37 58,722,839 Satt191 G_(18) 89.37 58,722,839 BARCSOYSSR_18_1767G_(18) 91.08 58,879,563 Sat_117 G_(18) 91.08 58,879,563BARC-010491-00654 G_(18) 93.00 59,279,444 BARC-010495-00656 G_(18) 93.2359,283,702 BARC-024251-04812 G_(18) 94.30 59,472,425 BARC-020069-04425G_(18) 96.31 59,797,088 BARC-062677-18004 G_(18) 97.32 59,995,654BARC-062769-18043 G_(18) 100.16 60,441,813 BARCSOYSSR_18_1853 G_(18)100.37 60,463,067 Sct_187 G_(18) 100.37 60,463,067 BARC-044363-08678G_(18) 100.44 60,487,624 BARCSOYSSR_18_1858 G_(18) 101.82 60,612,599Sat_064 G_(18) 101.82 60,612,599 BARC-054735-12156 G_(18) 102.3360,802,269 BARC-013647-01216 G_(18) 103.22 60,909,921 BARC-055537-13406G_(18) 103.40 61,041,397 BARC-039397-07314 G_(18) 103.55 61,188,102BARC-043995-08576 G_(18) 104.09 61,306,670 BARC-064703-18782 G_(18)105.53 61,480,202 BARC-049989-09280 G_(18) 105.85 61,591,089BARC-017669-03102 G_(18) 107.09 62,046,576 BARC-013305-00475 G_(18)107.09 62,259,025

In certain embodiments, multiple marker loci that collectively make upthe soybean cyst nematode resistance haplotype of interest areinvestigated. For example, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more of thevarious marker loci provided herein can comprise a soybean cyst nematoderesistance haplotype. In some embodiments, the haplotype comprises: twoor more marker locus comprising (a) at least one marker locus comprisesS08271-1-Q2 or a marker closely linked thereto on linkage group G; (b)at least one marker locus comprises P7659A-2 or a marker closely linkedthereto on linkage group G; (c) at least one marker locus comprisesS08051-1-Q1 or a marker closely linked thereto on linkage group G; (d)at least one marker locus comprises S07158-1-Q1 or a marker closelylinked thereto on linkage group G; (e) at least one marker locuscomprises S07159-1-Q1 or a marker closely linked thereto on linkagegroup G; (0 at least one marker locus comprises S06818-3-Q2 or a markerclosely linked thereto on linkage group G; (g) at least one marker locuscomprises S06820-1-Q3 or a marker closely linked thereto on linkagegroup 0; (h) at least one marker locus comprises S06821-1-Q2 or a markerclosely linked thereto on linkage group G; (i) at least one marker locuscomprises S16001-001-Q001 or a marker closely linked thereto on linkagegroup G; (j) at least one marker locus is between about marker Satt309and BARC-012285-01798 on linkage group G; (k) at least one marker locusis between about marker BARC-015371-01813 and BARCSOYSSR_(—)18_(—)0093on linkage group G; (l) at least one marker locus is between aboutmarker BARC-030055-06792 and BARC-025777-05064 on linkage group G; (m)the at least one marker locus is between about marker BARC-015371-01813and BARCSOYSSR_(—)18_(—)0093 on linkage group G; (n) at least one markerlocus is between about marker BARC-015371-01813 andBARCSOYSSR_(—)18_(—)0093 on linkage group G; or (o) at least one markerlocus comprises at least one of Gm18:926125; Gm18:1138152; Gm18:1517146;Gm18:1518206; Gm18:1520624; Gm18:1520675; Gm18:1520743; Gm18:1524498;Gm18:1548716; Gm18:1550153; Gm18:1550231; Gm18:1552799; Gm18:1554392;Gm18:1554570; Gm18:1554604; Gm18:1554689; Gm18:1555210; Gm18:1560043;Gm18:1560088; Gm18:1560390; Gm18:1560442; Gm18:1560784; Gm18:1561009;Gm18:1561190; Gm18:1561429; Gm18:1561725; Gm18:1562884; Gm18:1563153;Gm18:1564092; Gm18:1565225; Gm18:1565646; Gm18:1566882; Gm18:1567685;Gm18:1567843; Gm18:1568490; Gm18:1568999; Gm18:1569035; Gm18:1569146;Gm18:1570660; Gm18:1572368; Gm18:1577559; Gm18:1578727; Gm18:1579201;Gm18:1579270; Gm18:1579707; Gm18:1579708; Gm18:1581688; Gm18:1583772;Gm18:1584054; Gm18:1584659; Gm18:1589032; Gm18:1595321; Gm18:1598101;Gm18:1599717; Gm18:1599752; Gm18:1599841; Gm18:1600011; Gm18:1600033;Gm18:1600179; Gm18:1601192; Gm18:1601614; Gm18:1602244; Gm18:1603722;Gm18:1604031; Gm18:1605443; Gm18:1606442; Gm18:1606566; Gm18:1606647;Gm18:1609397; Gm18:1610935; Gm18:1612466; Gm18:1612553; Gm18:1614300;Gm18:1614960 Gm18:1618118; Gm18:1626263; Gm18:1626278; Gm18:1627202;Gm18:1627204; Gm18:1629930; Gm18:1634611; Gm18:1643225; Gm18:1653887;Gm18:1654681; Gm18:1654687; Gm18:1657025; Gm18:1680507; Gm18:1700832;Gm18:1700885; Gm18:1701854; Gm18:1702482; Gm18:1702563; Gm18:1702741;Gm18:1703321; Gm18:1706708; Gm18:1706842; Gm18:1707082; Gm18:1707115;Gm18:1707377; Gm18:1708549; Gm18:1717352; Gm18:1721829; Gm18:1723649;Gm18:1723650; Gm18:1724082; Gm18:172553; Gm18:1725630; Gm18:1725815;Gm18:1725932; Gm18:1725991; Gm18:1726068; Gm18:1727330; Gm18:1727343;Gm18:1727903; Gm18:1728146; Gm18:1728824; Gm18:1729347; Gm18:1729673;Gm18:1729866; Gm18:1730855; Gm18:1731068; Gm18:1731184; Gm18:1731725;Gm18:1731938; Gm18:1734691; Gm18:1735510; Gm18:1740118; Gm18:1747766;Gm18:1751156; Gm18:1752808; Gm18:1754310; Gm18:1754895; Gm18:1759167;Gm18:1759307; Gm18:1761263; Gm18:1762686; Gm18:1763519; Gm18:1768783;Gm18:1768805; Gm18:1769619; Gm18:1773903; Gm18:1773911; Gm18:1778021;Gm18:1783028; Gm18:1783194; Gm18:1783357; Gm18:1785320; Gm18:1787549;Gm18:1789215; Gm18:1789352; Gm18:1789553; Gm18:1789934; Gm18:1805509;Gm18:1859739; Gm18:1863987; Gm18:1864738; Gm18:1877951; Gm18:1881755;Gm18:1607524; Gm18:1888247; Gm18:1845911; Gm18:1846008; Gm18:1565826; orGm18:1918014; or a marker closely linked thereto on linkage group G.

In one embodiment, the method of identifying a first soybean plant or afirst soybean germplasm that displays improved resistance to soybeancyst nematode comprises detecting in the genome of the first soybeanplant or in the genome of the first soybean germplasm at least onehaplotype that is associated with the resistance, wherein the at leastone haplotype comprises at least two of the various marker loci providedherein. For example, one is more likely to get PI88788 Rhg1 if A, T isselected at S08271-1 and P7659-2 respectively. S07158-1 and S07159-1 areused in combination with S08051-1 to distinguish PI437654 and Pekinghaplotype.

In certain embodiments, two or more marker loci or haplotypes cancollectively make up a marker profile. The marker profile can compriseany two or more marker loci comprising: (a) at least one marker locuscomprises S08271-1-Q2 or a marker closely linked thereto on linkagegroup G; (b) at least one marker locus comprises P7659A-2 or a markerclosely linked thereto on linkage group G; (c) at least one marker locuscomprises S08051-1-Q1 or a marker closely linked thereto on linkagegroup G; (d) at least one marker locus comprises S07158-1-Q1 or a markerclosely linked thereto on linkage group G; (e) at least one marker locuscomprises S07159-1-Q1 or a marker closely linked thereto on linkagegroup G; (f) at least one marker locus comprises S06818-3-Q2 or a markerclosely linked thereto on linkage group G; (g) at least one marker locuscomprises S06820-1-Q3 or a marker closely linked thereto on linkagegroup G; (h) at least one marker locus comprises S06821-1-Q2 or a markerclosely linked thereto on linkage group G; (i) at least one marker locuscomprises S16001-001-Q001 or a marker closely linked thereto on linkagegroup G; (j) at least one marker locus is between about marker Satt309and BARC-012285-01798 on linkage group G; (k) at least one marker locusis between about marker BARC-015371-01813 and BARCSOYSSR_(—)18_(—)0093on linkage group G; (l) at least one marker locus is between aboutmarker BARC-030055-06792 and BARC-025777-05064 on linkage group G; (m)at least one marker locus is between about marker BARC-015371-01813 andBARCSOYSSR_(—)18_(—)0093 on linkage group G; (n) at least one markerlocus is between about marker BARC-015371-01813 andBARCSOYSSR_(—)18_(—)0093 on linkage group G; (o) at least one markerlocus comprises at least one of Gm18:926125; Gm18:1138152; Gm18:1517146;Gm18:1518206; Gm18:1520624; Gm18:1520675; Gm18:1520743; Gm18:1524498;Gm18:1548716; Gm18:1550153; Gm18:1550231; Gm18:1552799; Gm18:1554392;Gm18:1554570; Gm18:1554604; Gm18:1554689; Gm18:1555210; Gm18:1560043;Gm18:1560088; Gm18:1560390; Gm18:1560442; Gm18:1560784; Gm18:1561009;Gm18:1561190; Gm18:1561429; Gm18:1561725; Gm18:1562884; Gm18:1563153;Gm18:1564092; Gm18:1565225; Gm18:1565646; Gm18:1566882; Gm18:1567685;Gm18:1567843; Gm18:1568490; Gm18:1568999; Gm18:1569035; Gm18:1569146;Gm18:1570660; Gm18:1572368; Gm18:1577559; Gm18:1578727; Gm18:1579201;Gm18:1579270; Gm18:1579707; Gm18:1579708; Gm18:1581688; Gm18:1583772;Gm18:1584054; Gm18:1584659; Gm18:1589032; Gm18:1595321; Gm18:1598101;Gm18:1599717; Gm18:1599752; Gm18:1599841; Gm18:1600011; Gm18:1600033;Gm18:1600179; Gm18:1601192; Gm18:1601614; Gm18:1602244; Gm18:1603722;Gm18:1604031; Gm18:1605443; Gm18:1606442; Gm18:1606566; Gm18:1606647;Gm18:1609397; Gm18:1610935; Gm18:1612466; Gm18:1612553; Gm18:1614300;Gm18:1614960 Gm18:1618118; Gm18:1626263; Gm18:1626278; Gm18:1627202;Gm18:1627204; Gm18:1629930; Gm18:1634611; Gm18:1643225; Gm18:1653887;Gm18:1654681; Gm18:1654687; Gm18:1657025; Gm18:1680507; Gm18:1700832;Gm18:1700885; Gm18:1701854; Gm18:1702482; Gm18:1702563; Gm18:1702741;Gm18:1703321; Gm18:1706708; Gm18:1706842; Gm18:1707082; Gm18:1707115;Gm18:1707377; Gm18:1708549; Gm18:1717352; Gm18:1721829; Gm18:1723649;Gm18:1723650; Gm18:1724082; Gm18:172553; Gm18:1725630; Gm18:1725815;Gm18:1725932; Gm18:1725991; Gm18:1726068; Gm18:1727330; Gm18:1727343;Gm18:1727903; Gm18:1728146; Gm18:1728824; Gm18:1729347; Gm18:1729673;Gm18:1729866; Gm18:1730855; Gm18:1731068; Gm18:1731184; Gm18:1731725;Gm18:1731938; Gm18:1734691; Gm18:1735510; Gm18:1740118; Gm18:1747766;Gm18:1751156; Gm18:1752808; Gm18:1754310; Gm18:1754895; Gm18:1759167;Gm18:1759307; Gm18:1761263; Gm18:1762686; Gm18:1763519; Gm18:1768783;Gm18:1768805; Gm18:1769619; Gm18:1773903; Gm18:1773911; Gm18:1778021;Gm18:1783028; Gm18:1783194; Gm18:1783357; Gm18:1785320; Gm18:1787549;Gm18:1789215; Gm18:1789352; Gm18:1789553; Gm18:1789934; Gm18:1805509;Gm18:1859739; Gm18:1863987; Gm18:1864738; Gm18:1877951; Gm18:1881755;Gm18:1607524; Gm18:1888247; Gm18:1845911; Gm18:1846008; Gm18:1565826; orGm18:1918014; or a marker closely linked thereto on linkage group G; (p)any marker loci associated with the rhg1 locus on linkage group G; (q)any marker loci associated with the rhg2 locus on linkage group M; (r)any marker loci associated with the rhg4 locus on linkage group A2;and/or (s) any marker loci associated with resistance to soybean cystnematode.

Any of the marker loci in any of the genomic loci disclosed herein canbe combined in the marker profile. For example, the marker profile cancomprise 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,20, or more marker loci or haplotypes associated with resistance tosoybean cyst nematode provided herein.

In one embodiment, a method of identifying a first soybean plant or afirst soybean germplasm that displays improved resistance to soybeancyst nematode comprises detecting in the genome of the first soybeanplant or in the genome of the first soybean germplasm at least onemarker profile that is associated with the resistance, wherein the atleast one marker profile comprises at least two of the various markerloci provided herein.

Not only can one detect the various markers provided herein, it isrecognized that one could detect any markers that are closely linked tothe various markers discussed herein.

In addition to the markers discussed herein, information regardinguseful soybean markers can be found, for example, on the USDA's Soybasewebsite, available at www.soybase.org. One of skill in the art willrecognize that the identification of favorable marker alleles may begermplasm-specific. The determination of which marker alleles correlatewith resistance (or susceptibility) is determined for the particulargermplasm under study. One of skill will also recognize that methods foridentifying the favorable alleles are routine and well known in the art,and furthermore, that the identification and use of such favorablealleles is well within the scope of the invention.

Various methods are provided to identify soybean plants and/or germplasmwith improved resistance to soybean cyst nematode. In one embodiment,the method of identifying comprises detecting at least one marker locusassociated with resistance to soybean cyst nematode. The term“associated with” in connection with a relationship between a markerlocus and a phenotype refers to a statistically significant dependenceof marker frequency with respect to a quantitative scale or qualitativegradation of the phenotype. Thus, an allele of a marker is associatedwith a trait of interest when the allele of the marker locus and thetrait phenotypes are found together in the progeny of an organism moreoften than if the marker genotypes and trait phenotypes segregatedseparately.

Any combination of the marker loci provided herein can be used in themethods to identify a soybean plant or soybean germplasm that displaysimproved resistance to soybean cyst nematode. Any one marker locus orany combination of the markers set forth in Table 1, or any closelylinked marker can be used to aid in identifying and selecting soybeanplants or soybean germplasm with improved resistance to soybean cystnematode.

In one embodiment, a method of identifying a first soybean plant or afirst soybean germplasm that displays improved resistance to soybeancyst nematode is provided. The method comprises detecting in the genomeof the first soybean plant or first soybean germplasm at least onemarker locus that is associated with resistance. In such a method, theat least one marker locus comprises (a) at least one marker locuscomprises S08271-1-Q2 or a marker closely linked thereto on linkagegroup G; (b) at least one marker locus comprises P7659A-2 or a markerclosely linked thereto on linkage group G; (c) at least one marker locuscomprises S08051-1-Q1 or a marker closely linked thereto on linkagegroup G; (d) at least one marker locus comprises S07158-1-Q1 or a markerclosely linked thereto on linkage group G; (e) at least one marker locuscomprises S07159-1-Q1 or a marker closely linked thereto on linkagegroup G; (f) at least one marker locus comprises S06818-3-Q2 or a markerclosely linked thereto on linkage group G; (g) at least one marker locuscomprises S06820-1-Q3 or a marker closely linked thereto on linkagegroup G; (h) at least one marker locus comprises S06821-1-Q2 or a markerclosely linked thereto on linkage group G; (i) at least one marker locuscomprises S16001-001-Q001 or a marker closely linked thereto on linkagegroup G; (j) at least one marker locus is between about marker Satt309and BARC-012285-01798 on linkage group G; (k) at least one marker locusis between about marker BARC-015371-01813 and BARCSOYSSR_(—)18_(—)0093on linkage group G; (l) at least one marker locus is between aboutmarker BARC-030055-06792 and BARC-025777-05064 on linkage group G; (m)at least one marker locus is between about marker BARC-015371-01813 andBARCSOYSSR_(—)18_(—)0093 on linkage group G; (n) at least one markerlocus is between about marker BARC-015371-01813 andBARCSOYSSR_(—)18_(—)0093 on linkage group G; or (o) at least one markerlocus comprises at least one of Gm18:926125; Gm18:1138152; Gm18:1517146;Gm18:1518206; Gm18:1520624; Gm18:1520675; Gm18:1520743; Gm18:1524498;Gm18:1548716; Gm18:1550153; Gm18:1550231; Gm18:1552799; Gm18:1554392;Gm18:1554570; Gm18:1554604; Gm18:1554689; Gm18:1555210; Gm18:1560043;Gm18:1560088; Gm18:1560390; Gm18:1560442; Gm18:1560784; Gm18:1561009;Gm18:1561190; Gm18:1561429; Gm18:1561725; Gm18:1562884; Gm18:1563153;Gm18:1564092; Gm18:1565225; Gm18:1565646; Gm18:1566882; Gm18:1567685;Gm18:1567843; Gm18:1568490; Gm18:1568999; Gm18:1569035; Gm18:1569146;Gm18:1570660; Gm18:1572368; Gm18:1577559; Gm18:1578727; Gm18:1579201;Gm18:1579270; Gm18:1579707; Gm18:1579708; Gm18:1581688; Gm18:1583772;Gm18:1584054; Gm18:1584659; Gm18:1589032; Gm18:1595321; Gm18:1598101;Gm18:1599717; Gm18:1599752; Gm18:1599841; Gm18:1600011; Gm18:1600033;Gm18:1600179; Gm18:1601192; Gm18:1601614; Gm18:1602244; Gm18:1603722;Gm18:1604031; Gm18:1605443; Gm18:1606442; Gm18:1606566; Gm18:1606647;Gm18:1609397; Gm18:1610935; Gm18:1612466; Gm18:1612553; Gm18:1614300;Gm18:1614960 Gm18:1618118; Gm18:1626263; Gm18:1626278; Gm18:1627202;Gm18:1627204; Gm18:1629930; Gm18:1634611; Gm18:1643225; Gm18:1653887;Gm18:1654681; Gm18:1654687; Gm18:1657025; Gm18:1680507; Gm18:1700832;Gm18:1700885; Gm18:1701854; Gm18:1702482; Gm18:1702563; Gm18:1702741;Gm18:1703321; Gm18:1706708; Gm18:1706842; Gm18:1707082; Gm18:1707115;Gm18:1707377; Gm18:1708549; Gm18:1717352; Gm18:1721829; Gm18:1723649;Gm18:1723650; Gm18:1724082; Gm18:172553; Gm18:1725630; Gm18:1725815;Gm18:1725932; Gm18:1725991; Gm18:1726068; Gm18:1727330; Gm18:1727343;Gm18:1727903; Gm18:1728146; Gm18:1728824; Gm18:1729347; Gm18:1729673;Gm18:1729866; Gm18:1730855; Gm18:1731068; Gm18:1731184; Gm18:1731725;Gm18:1731938; Gm18:1734691; Gm18:1735510; Gm18:1740118; Gm18:1747766;Gm18:1751156; Gm18:1752808; Gm18:1754310; Gm18:1754895; Gm18:1759167;Gm18:1759307; Gm18:1761263; Gm18:1762686; Gm18:1763519; Gm18:1768783;Gm18:1768805; Gm18:1769619; Gm18:1773903; Gm18:1773911; Gm18:1778021;Gm18:1783028; Gm18:1783194; Gm18:1783357; Gm18:1785320; Gm18:1787549;Gm18:1789215; Gm18:1789352; Gm18:1789553; Gm18:1789934; Gm18:1805509;Gm18:1859739; Gm18:1863987; Gm18:1864738; Gm18:1877951; Gm18:1881755;Gm18:1607524; Gm18:1888247; Gm18:1845911; Gm18:1846008; Gm18:1565826; orGm18:1918014; or a marker closely linked thereto on linkage group G.

In other embodiments, two or more marker loci are detected in themethod. In a specific embodiment, the germplasm is a soybean variety.

In other embodiments, the method further comprises crossing the selectedfirst soybean plant or first soybean germplasm with a second soybeanplant or second soybean germplasm. In a further embodiment of themethod, the second soybean plant or second soybean germplasm comprisesan exotic soybean strain or an elite soybean strain.

In specific embodiments, the first soybean plant or first soybeangermplasm comprises a soybean variety. Any soybean line known to the artor disclosed herein may be used. Non-limiting examples of soybeanvarieties and their associated soybean cyst nematode resistance allelesencompassed by the methods are provided herein.

In another embodiment, the detection method comprises amplifying atleast one marker locus and detecting the resulting amplified markeramplicon. In such a method, amplifying comprises (a) admixing anamplification primer or amplification primer pair for each marker locusbeing amplified with a nucleic acid isolated from the first soybeanplant or the first soybean germplasm such that the primer or primer pairis complementary or partially complementary to a variant or fragment ofthe genomic locus comprising the marker locus and is capable ofinitiating DNA polymerization by a DNA polymerase using the soybeannucleic acid as a template; and (b) extending the primer or primer pairin a DNA polymerization reaction comprising a DNA polymerase and atemplate nucleic acid to generate at least one amplicon. In such amethod, the primer or primer pair can comprise a variant or fragment ofone or more of the genomic loci provided herein.

In one embodiment, the method involves amplifying a variant or fragmentof one or more polynucleotides comprising SEQ ID NOS: 1-171 or variantsor fragments thereof. In one embodiment, the primer or primer pair cancomprise a variant or fragment of one or more polynucleotides comprisingSEQ ID NOS: 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114,115, 116, 117, 118, 119, 120, 138, 139, 142, 143, 146, 147, 150, 151,154, 155, 158, 159, 162, 163, 166, 167, 170 or 171 or complementsthereof. In specific embodiments, the primer or primer pair comprises anucleic acid sequence comprising SEQ ID NOS: SEQ ID NO: 1, 2, 3, 4, 5,6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42,43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60,61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,79, 80, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 136, 137,140, 141, 144, 145, 148, 149, 152, 153, 156, 157, 160, 161, 164, 165,168, or 169 or variants or fragments thereof.

In a specific embodiment, the primer pair comprises SEQ ID NOS: 81 and82; SEQ ID NOS: 87 and 88; SEQ ID NOS: 89 and 90; SEQ ID NOS: 91 and 92;SEQ ID NOS: 93 and 94; SEQ ID NOS:95 and 96; SEQ ID NOS: 97 and 98; SEQID NOS: 99 and 100; SEQ ID NOS: 101 and 102, SEQ ID NOS: 121 and 122;SEQ ID NO: 121 and 123; SEQ ID NO:124 and 125; SEQ ID NO: 126 and 127;SEQ ID NO: 128 and 129; SEQ ID NO: 130 and 131, SEQ ID NOS: 136 and 137;SEQ ID NOS: 140 and 141; SEQ ID NOS: 144 and 145; SEQ ID NOS: 148 and149; SEQ ID NOS: 152 and 153; SEQ ID NOS: 156 and 157; SEQ ID NOS: 160and 161; SEQ ID NOS: 164 and 165; or SEQ ID NOS:168 and 169.

In another embodiment, the method further comprises providing one ormore labeled nucleic acid probes suitable for detection of each markerlocus being amplified. In such a method, the labeled nucleic acid probecan comprise a sequence comprising a variant or fragment of one or moreof the genomic loci provided herein. In one embodiment, the labelednucleic acid probe can comprise a sequence comprising a variant orfragment of one or more polynucleotides comprising SEQ ID NOS: 103, 104,105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118,119, 120, 138, 139, 142, 143, 146, 147, 150, 151, 154, 155, 158, 159,162, 163, 166, 167, 170 or 171 or complements thereof. In specificembodiments, the labeled nucleic acid probe comprises a nucleic acidsequence comprising SEQ ID NOS: 81, 82, 83, 84, 85, 86, 87, 88, 89, 100,101, 102, 132, 133, 134, 135 or variants or fragments thereof.

Non-limiting examples of primers, probes, genomic loci and ampliconsthat can be used in the methods and compositions provided herein aresummarized in Tables 3, 4, 5 and 6, respectively.

TABLE 3 Non-Limiting Examples of Primer Sequences. Linkage Group PrimerSEQ ID Allele (ch) Marker ID Name NO Primer Sequence (Res/Sus) GS08271-1-Q2 A/T (P10355B-1) S08271-1  1 CATTGTTGCCAAGTAATAC F1TACTATATAAATTC S08271-  2 TCAAGTATCGCGCAAGCTC R1 S08271-  3attcgcccttcatggtttct F2 S08271-  4 ctgagtcttatcattctgtggattg F3 S08271- 5 gcaagctcctgcaaggtatt R2 S08271-  6 Catggtttctcttatcttatracattg R3aS08271-  7 CAATTCATGGTTTCTCTTAT R3a RACATT 137362-  8TCAAGTATCGCGCAAGCTC 1 137363-  9 CATGGTTTCTCTTATCTTAT 2 RACATTG 137364-10 CAATTCATGGTTTCTCTTAT 3 RACATT 137365- 11 GCAAGCTCCTGCAAGGTAT F2 TAT72625- 12 CTTATCTTATRACATTGTTG R2 CCAAG 137366- 13 TCTCTTATRACATTGTTGCCR2-2 AAG 137367- 14 CCACTGTCCCTGCTCCTG F3 137368- 15GGTTTCTCTTATCTTATRAC R3 ATTGTTG 137369- 16 CATGGTTTCTCTTATRACAT R3-3TGTTG 89472 17 CGCGCAAGCTCCTGCAAG GTATTATAT 19392 18CATGGTTTCTCTTATCTTAT RACATTGTTGCCAAG 19393 19 CAATTCATGGTTTCTCTTATRACATTGTTGCCAAG P10366B- 20 GACCTTGCGCGATACTTGA 1R S08271- 21tcaagtatcgcgcaagctc F4 S08271- 22 cattgttgccaagtaatactactatataaat F1 tcS08271- 23 attcgcccttcatggtttct F2 S08271- 24 ctgagtcttatcattctgtggattgF3 S08271- 25 cattgttgccaagtaatactactatataaat F1 tc S08271- 26Catggtttctcttatcttatracattg R3 S08271- 27 CAATTCATGGTTTCTCTT R3 ATRACATTS08271- 28 tcaagtatcgcgcaagctc R1 S08271- 29 gcaagctcctgcaaggtatt R2S08271- 30 gcaagctcctgcaaggtatt R2 S08271- 31 tcaagtatcgcgcaagctc R1 GP7659a-2 A/G (S08052-1-Q1) 136879 32 ATGAAGCTCCACCATTTGC T 136880 33TGGGGGAACATATACCTTG AA 136881 34 TGTCGGGTATGTTTCCATG A 136882 35CATGGGGGAACATATACCT TG 136883 36 TGTGGTACATGGGGGAAC A 88258 37TTTCCATGAAGCTCCACCA TTTGCT 88260 38 TGTCTATCCTGTAGGTGGC TATTAAGATGCTGA G508051-1-Q1 GA/AC 136874 39 TGGCAACAAAATCAGAACC A 136875 40TGTTTTTAAGCCCGATGGA G 82585 41 TCCAGAAAGTGGGGTAAG AATGTCTGAGAA 82586 42GGCATGTTTTTAAGCCCGA antisense TGGAGTA 82586 43 TACTCCATCGGGCTTAAAAACATGCC 136876, 44 ATGGCAACAAAATCAGAAC p7659A- CA 1-F3 136877, 45TGGAAATTTCTCTGCAACC p7659A- A 1-R3 136878, 46 TGTTGATCTCGTGGTGGAAp7659A- A 1-R4 G S07158-1-Q1 TG/GT 137377 47 AAGTTCCAATTGTTTCATCT AAATCC137378 48 CCGTCAATCACATGAGTCC A 137375, 49 ACCACTTACTGTCATTTTGG p5219A-TTCTT 1-F1 137376, 50 TCCGTCAATCACATGAGTC p5219A- C 1-R1 137379, 51CACCTTGTCACATTAGTTG p5219A- CTGA 1-F3 137380, 52 TCACATGAGTCCAAAATGAp5219A- AAAA 1-R3 G S07159-1-Q1 T/A 136857,F 53 TGGTACCATGCCTCCCTTTA 2136858, 54 CCATTTTGTATTCCCTCATG R2 C 82575 55 TGTGGGCAGGAGGTTTATGAGTTTATGGTA 82576 56 CAATGAAGTTAAGCAAGTT AATGATGACCATTTTG 136859, 57TGGGCAGGAGGTTTATGA F3 GT 136860, 58 GGCAATGGGGTACGAAGT R3 TT 136861, 59TTCTGTGGGCAGGAGGTTT F4 A 136862, 60 GAAGAGCCTCTGGGCAAT R4 G GS06818-3-Q2 C/G 142732 61 TCATTTGATCCTTATACCTG CACA 142733 62ACTTTTTAATCCGTTTTAAT CTCTGC S06818- 63 CATTTGATCCTTATACCTGC 3-Q1F ACAS06818- 64 TGCAGTGTAGGACTAATAT 3-Q1R GCGTTA S06818- 65GAAGGATGATGACTGTTAT 3-Q3F TCAGAATTT S06818- 66 GCAGTGTAGGACTAATATG 3-Q3RCGTTAAAA G S06820-1-Q3 C/T 142736 67 TGGGACTGACTGCTATGAC TGA 142737 68AGCTCGTGTACCAGCCTGA A S06820- 69 TTGGGAAAAGAAGTGCAT 1-Q1F GG S06820- 70CGTGTACCAGCCTGAAATG 1-Q1R A S06820- 71 CATGTGGGACTGACTGCTA 1-Q2F TGS06820- 72 TCGTGTACCAGCCTGAAAT 1-Q2R G G S06821-1-Q2 A/C 142740 73GCCAAATTGAATCTAGGCA AA 142741 74 TCACGTGTCCTCTCCAGAA A S06821- 75AAAACTATAAATGAACTTG 1-Q1F GGGTGA S06821- 76 GCTTTTCACGTGTCCTCTCC 1-Q1RS06821- 77 TCATCACCTGATATGATCTT 1-Q3F AATGGA S06821- 78TGATGCTAGCTTTTCACGT 1-Q3R GTC G S16001-001- C/A Q001 S16001- 79TTCCACCAACAAACTGGTG F001 A S16001- 80 CATTTTGACCATGCCCTTG R001

TABLE 4 Non-Limiting Examples of Probe Sequences. (R) SEQ ID (R) SEQ IDProbe 1 or Probe 1 NO for Probe 2 or Probe 2 NO for Markers Name (S)Sequence Probe 1 Name (S) Sequence Probe 2 S08271-1-Q2 (P10355B-1)S08271- R TGGGTTTCAG  81 S08271-1- S TGGGTTTCTG  82 1-PB1 ATAAC PB2ATAACC S08271-1- 6FAM-  83 PB1 TGGGTTTCA GATAAC S08271-1- 6FAM-  84 PB3accacggttatcTg aa S08271-1- VIC-  85 PB2 TGGGTTTCT GATAACC S08271-1-VIC-  86 PB4 accacggttatcAg aa P7659A-2 (S08052-1- Q1) 137434 RCTACATCTCC  87 137435 S TCTACATTTCC  88 TCTTTG TCTTTG S08051-1-Q1(P7659A-1) 141803 R CATTTTTCAT  89 141804 S CATTTTTCAGT  90 CGCACTTTGCACTTT S07158-1-Q1 (P5219A-1) 125317 S CATATGTCAG  91 125318 RCATATTGCAG  92 TACTATAAC TACTATAA S07159-1-Q1 (P5219A-2) 102398 STGTTGATAAA  93 102399 R TGTTGATAAA  94 CCATATATG CCTTATATG S06818-3-Q2142734 R CTTGCCTACA  95 142735 S CTTGCGTACA  96 CATACA CATAC S06820-1-Q3142738 R TATCACGCAA  97 142739 S ATCACACAAC  98 CCAGTTC CAGTTCS06821-1-Q2 142742 R TCCTCTATTG  99 142743 S ATCCTCGATT 100 AATCTTGAATCT S16001-001- Q001 S16001- R atatgctaccaAt 101 S16001- SatatgctaccaCt 102 001- acagc 001-X001 acagct X002

TABLE 5Non-Limiting Examples of Genomic Loci Comprising the Various Marker LociProvided Herein. SEQ ID Marker NO Name (Res/Sus)Reference Sequence [Res/Sus] SEQ ID NO S08271-1- A/TCTGAAATGCAACGCAAATTCGAGTTTAGTAGAAACTTATCATCCAAAAT 103, 104 Q2TAAAATTGAAAACTTTAATACAAATGCACATTTTGGAGCCATTCATGTS respectively (P10355B-ATCTCTTGGTCTGAGTCTTATCATTCTGTGGATTGAATTCATGGTTTCTC 1)TTATVACATTGTTGCCAAGTAATACTACTATATAAATTCAGATTTGGGTTTC[A/T]GATAACCGTGGTCGTTARTACTATATATATAATACCTTGCAGGAGCTTGCGCGATACTTGAAACAGGAGCAGGGACAGTGGAAAATAAAGGAGCCATAGCRCCATCTGCTTGCTTATGTAATGTAACCCAATCTGTCTATATTTYAATACACACCCCATTACGATAAAATTATGCTAGGGCCTAATTTG AATTGATTTCT P7659A-2T/C CTCTGTATTTTATGGATGCTCATTGCTTGTGAATCATCATTGGGGGGTT 105, 106(S08052-1- GTAATAGCATGAAATGATGGAGAACAGGTGATTGAAGGCATATCTCAT respectivelyQ1 GTGGTACATGGGGGAACATATACCTTGAAAACTCACAGAACTATATATTTTATTGAACTGTCTATCCTGTAGGTGGCTATTAAGATGCTGAGTTAATCTACAT[T/C]TCCTCTTTGTATTAAAAAGTTGTTTCATGTACTAGCAAATGGTGGAGCTTCATGGAAACATACCCGACATCTAAATTTCTTATTATTGTTGCTTTATCATTATTTTCTGTGGCCCAATTGATGTATTATGCCCCTATGTTTTACTATCTTATTGAATTCAGAAGTATTGATTGCAGGTGGATAATAAAG CTGCAGTCCTT S08051-1-GT/TC AATAGATCTAATTTGTTAAGCTTTATTTACCAGAGTTACCAAACCATCTG 107, 108 Q1TGAGAAATATCCTTCATTCCGTGAAAGATCTGAAAATGTTGATCTCGTG respectively(P7659A-1) GTGGAAATTTCTCTGCAACCATGGCATGTTTTTAAGCCCGATGGAGTAAGATAACTCTCTGGCACTCTTTAATTTATTTATGCTTTTTCAGGCATTTTTCA[GT][TC]GCACTTTTTGTGATATGGTTCTGATTTTGTTGCCATTAACAATTTGCTTGGTACTTATTCTGTGACAGGTGATTTTATTCTCAGACATTCTTACCCCACTTTCTGGAATGAATATACCCTTTGATATTGTGAAGGGTAAGGGTCCTGTTATATTTGATCCTATTCACACAGCTGCCCAGGTTGATCAAGTG AGGGAGTT S07158-1-GT/TG TTAAACAGTTAACAATATGTTTGCTAGCCTACACACAAATCATGATTCA 109, 110 Q1GTACACAACCATTTTGGTCCCTGAAAGTATATCACCTTGTCACATTAGTT respectively(P5219A-1) GCTGAAACTAAGGAAATACTAAATAAGTTCTAAAAGTTCCAATTGTTTCATCTAAATCCTAAATTTAACCACTTACTGTCATTTTGGTTCTTAAACATAT[GT][TG]CAGTACTATAACTTAAATCAAACATTTTTTTTTTTTCATTTTGGACTCATGTGATTGACGGATTTTACTTCGAAGAACTTATTTAGAAGTTTCATAGGTAGTATGTGACAGCACCGTACAGTGTACACTTTCACAAACTAAAACTAAATCGGTGGTTTACTCAATCATACTCAATAATTCAGAAAAGAATC ATACATAAA S07159-1-T/A AGACAGCCTATGTGTAACACTTAAAAGTTATCACCATGTGACCATGAAG 111, 112 Q1TCACAGGTTTGAGTTGTGGAATCAGCCTCTTGAAAATGCAAGGAAAGG respectively (P5219A-2)CTGTCTACTATACAGTATAAACCCACACAGAGATCTGACCGTTCTGTGGGCAGGAGGTTTATGAGTTTATGGTRCATGCCTCCCTTTATTTTGTTGATAAACC[T/A]TATATGGTACTAATAGCATGAGGGAATCAAAATGGTCATCATTAACTTGCTTAACTTCATTGACGTATGTTATCTTGTCAAAGATATCATGAGGCATATAATAATGTTATAAAAAACTTACACACTATCAACACCTATTGGTGACCATTGTACAAGTGYCTATAATAAAGCCTGTAAACATAACKTACC AATGTTGAAAG S06818-3-G/C TACATATAGCATAAATTATCTAATTCTCTAATCTATACAAATCAAGGTTT 113, 114 Q2AATTACTCATTTGGTCTCTTTACCTGCACAATCTTTATGCTTTATTCCTTG respectivelyTATCTAGAAACTACTTGTTTTAATCTMTACACATATACTTTTTAATCCGTTTTAATCTCTGCAGTGTAGGACTAATATGCGTTAAAAAGTGTATGTGTA[G/C]GCAAGTAGTTTCTAGGCATAGGAACTAAAACGTAAAGATTGTGCAGGTATAAGGATCAAATGAGTAATTAAACCTAAAAAAAATTCTGAATAACAGTCATCATCCTTCTATGAACTATCCTACCCTAGCATTTTTGGGATTGACCGCTACATGCTACCATMCAAGATTGATAACTATGATTACCATATGCA GGAAAGGAT S06820-1-G/A TAGTTTTAGGGTTAGAATGAACCATGCTAGATTGTTGTCTTTACTTTAGT 115, 116 Q3ATTTTTTCATGTTTTTGAAATGTTAAGTGATGCTAGTTGAGTTTATGTTG respectivelyAAGATTTTTATTGTTCAGGCTGTTAATTACATGTGGGACTGACTGCTATGACTGAGTCTTGGGAAAAGAAGTGCATGGCTTTATGTTTATGTAATATCAC[G/A]CAACCAGTTCATTTAAATCAATTTCCTGATAAAAGCATGCAATTCATTTCAGGCTGGTACACGAGCTCTGAAAAGGAAGGCATGGGAGCAGCTGGCCTTTGAAGAGGGTATGTTAATTGTTATACGTYATTACTTTGGGGCTTTAGATGGGATGATCTTCAAAGATGTGCTCTTTTAGATGAATGGTA CAAAATAGAAAT S06821-1-T/G TATGAAGAAGCTGGAACTCCTGTTATTAAGGAGAAGGATGAGGAMAA 117, 118 Q2TTGTGGAAATATTGTCAATGATGAAGAACAGGTGATGCAAATTCCAAG respectivelyCCCATGCTCTATGTCATCATCACCTGATATGATCTTAATGGAGTTGAAAAAAGCCAAATTGAATCTAGGCAAAACTATAAATGAACTTGGGGTGATACAATCCTC[T/G]ATTGAATCTTTGAATAAGAAGATGAAGAAGGAGAAAAATTTTCTGGAGAGGACACGTGAAAAGCTAGCATCAAAGTTTGCAGCAGAATCTGCTCAAGAGAGGGTCCAAGAGCAAACAAGATTGAATCCACCGGCCCCTCATGTAGAGTTCACCTTTGGTAACCCTGCWAATAATTTCAATT CTGATTCTGGGCAGTGCAAS16001- C/A CTCCTTTGCCAAGTCCCTKCAGAGCAAGTGCCCCAGAAGTGGAAATGA 119, 120001-Q001 CGATTTACTCGAACCCCTTGACCTTCAAACTCCTACCCATTTTGATAACC respectivelyTATACTTCCAGAATTTACTGGACAAAAAGGGTCTTCTCCATTCCGATCWGAAGCTGTTCAATGGTGATTCCACCAACAAACTGGTGAAGAAATATGCTACCA[C/A]TACAGCTGCATTCTTTAAAGACTTTGCCAAGGGCATGGTCAAAATGAGCAATATCAAGCCTCTAACAGGAAGCGAGGGGCAGATCAGAATCAATTGCAGRAAAGTCAATTAAGCATTAGCGTACTATATATGTCTATCCATRCTTATATTTATCTCCAATGATCCATCTTTCTTTACAAAATTATGT ATTCTCTAATCTM

TABLE 6 Non-limiting Examples of Amplicons Comprising the Various MarkerAmplicon Linkage SEQ ID Amplicon Marker Group Primer Primer NOAmplicon Sequence Size Name (cm) 1 2 (R/S) [Res/Sus] (bp) S08271-1- GCATTGTT TCAAGTAT CATTGTTGCCAAGTAATACTACTATA 108 Q2 GCCAAGT CGCGCAAGTAAATTCAGATTTGGGTTTC[A/T]GA (P10355B- AATACTA CTC (SEQTAACCGTGGTCGTTARTACTATATAT 1) CTATATA ID NO: ATAATACCTTGCAGGAGCTTGCGCGAATTC 137) ATACTTGA (SEQ ID NO: 138, (SEQ ID 139 respectively) NO 136)P7659A-2 G ATGAAGC TGGGGGA TGGGGGAACATATACCTTGAAAACT 149 TCCACCAACATATAC CACAGAACTATATATTTTATTGAACT TTTGCT CTTGAAGTCTATCCTGTAGGTGGCTATTAAG (SEQ ID (SEQ ID ATGCTGAGTTAATCTACAT[T/C]TCCNO 140)  NO 141) TCTTTGTATTAAAAAGTTGTTTCATG TACTAGCAAATGGTGGAGCTTCAT(SEQ ID NO 142, 143 respectively) S08051-1- G TGGCAAC TGTTTTTAATGTTTTTAAGCCCGATGGAGTAAGA 112 Q1 AAAATCA GCCCGATGTAACTCTCTGGCACTCTTTAATTTAT (P7659A- GAACCA GAG (SEQTTATGCTTTTTCAGGCATTTTTCA[GT] 1) (SEQ ID ID NO  [TC]GACTTTTTGTGATATGGTTCTNO 144) 145) GATTTTGTTGCCA (SEQ ID NO  146, 147 respectively) S07158-1-G AAGTTCC CCGTCAAT AAGTTCCAATTGTTTCATCTAAATCC 130 Q1 AATTGTT CACATGAGTAAATTTAACCACTTACTGTCATTTT (P5219A- TCATCTA TCCA (SEQGGTTCTTAAACATAT[GT][TG]CAGT 1) AATCC(SEQ ID NO ACTATAACTTAAATCAAACATTTTTT ID NO 149) TTTTTTCATTTTGGACTCATGTGATT 148)GACGG (SEQ ID NO 150, 151 respectively) S07159-1- G TGGTACC CCATTTTGTTGGTRCATGCCTCCCTTTATTTTGTT  70 Q1 ATGCCTC ATTCCCTCGATAAACC[T/A]TATATGGTACTAAT (P5219A- CCTTTA ATGC (SEQAGCATGAGGGAATCAAAATGG 2) (SEQ ID ID NO  (SEQ ID NO 154, 155  NO 152)153) respectively) S06818-3- G TCATTTG ACTTTTTAAACTTTTTAATCCGTTTTAATCTCTGC 127 Q2 ATCCTTAT TCCGTTTTAAGTGTAGGACTAATATGCGTTAAAA ACCTGCA ATCTCTGC AGTGTATGTGTA[G/C]GCAAGTAGTCA (SEQ (SEQ ID  TTCTAGGCATAGGAACTAAAACGTA ID NO NO 157)AAGATTGTGCAGGTATAAGGATCAA 156) ATGA (SEQ ID NO 158, 159 respectively)506820-1- G TGGGACT AGCTCGTG TGGGACTGACTGCTATGACTGAGTC 135 Q3 GACTGCTTACCAGCC TTGGGAAAAGAAGTGCATGGCTTTA ATGACTG TGAATGTTTATGTAATATCAC[G/A]CAACC A (SEQ ID (SEQ ID AGTTCATTTAAATCAATTTCCTGATA NO 160) NO 161) AAAGCATGCAATTCATTTCAGGCTGGTACACGAGCT (SEQ ID NO  162, 163 respectively) S06821-1- G GCCAAATTCACGTGT GCCAAATTGAATCTAGGCAAAACTA 113 Q2 TGAATCT CCTCTCCATAAATGAACTTGGGGTGATACAATC AGGCAAA GAAA (SEQ CTC[T/G[ATTGAATCTTTGAATAAGA(SEQ ID ID NO  AGATGAAGAAGGAGAAAAATTTTCT NO 164) 165)GGAGAGGACACGTGA (SEQ ID NO 166, 167 respectively) S16001- G TTCCACCCATTTTGA TTCCACCAACAAACTGGTGAAGAAA  82 001-Q001 AACAAAC CCATGCCCTATGCTACCA[C/A]TACAGCTGCATT TGGTGA TTG (SEQ CTTTAAAGACTTTGCCAAGGGCATG(SEQ ID  ID NO  GTCAAAATG (SEQ ID NO  NO 168) 169)170, 171, respectively)

In another embodiment, the method of detecting comprises DNA sequencingof at least one of the marker loci provided herein. As used herein,“sequencing” refers to sequencing methods for determining the order ofnucleotides in a molecule of DNA. Any DNA sequencing method known in theart can be used in the methods provided herein. Non-limiting examples ofDNA sequencing methods useful in the methods provided herein includeNext Generation Sequencing (NGS) technologies, for example, as describedin Egan, A. N, et al. (2012) American Journal of Botany 99(2):175-185;genotyping by sequencing (GBS) methods, for example, as described inElshire, R. J., et al. (2011) PLoS ONE 6(5):e19379; Molecular InversionProbe (MIP) genotyping, as described, for example, in Hardenbol, P., etal. (2003) Nature Biotechnology 21(6):673-678; or high throughputgenotyping by whole-genome resequencing, as described, for example inHuang, X et al., (2009) Genome Research 19:1068-1076. Each of the abovereferences is incorporated by reference in their entirety herein.

An active variant of any one of SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45,46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63,64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81,82, 83, 84, 85, 86, 87, 88, 89, 100, 101, 102, 103, 104, 105, 106, 107,108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121,122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135,136, 137, 140, 141, 144, 145, 148, 149, 152, 153, 156, 157, 160, 161,164, 165, 168, 169, 138, 139, 142, 143, 146, 147, 150, 151, 154, 155,158, 159, 162, 163, 166, 167, 170 or 171 can comprise a polynucleotidehaving at least 75%, 80% 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%,98% or 99% sequence identity to SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45,46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63,64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81,82, 83, 84, 85, 86, 87, 88, 89, 100, 101, 102, 103, 104, 105, 106, 107,108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121,122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, or 135as long as it is capable of amplifying and/or detecting the marker locusof interest. By “fragment” is intended a portion of the polynucleotide.A fragment or portion can comprise at least 5, 6, 7, 8, 9, 10, 11, 12,13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 50, 75, 100, 150, 200, 250,300, 350, 400 contiguous nucleotides of SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61,62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79,80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 100, 101, 102, 103, 104, 105,106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119,120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133,134, 135, 136, 137, 140, 141, 144, 145, 148, 149, 152, 153, 156, 157,160, 161, 164, 165, 168, 169, 138, 139, 142, 143, 146, 147, 150, 151,154, 155, 158, 159, 162, 163, 166, 167, 170 or 171 as long as it iscapable of amplifying and/or detecting the marker locus of interest.

Unless otherwise stated, sequence identity/similarity values providedherein refer to the value obtained using GAP Version 10 using thefollowing parameters: % identity and % similarity for a nucleotidesequence using GAP Weight of 50 and Length Weight of 3, and thenwsgapdna.cmp scoring matrix; or any equivalent program thereof. By“equivalent program” is intended any sequence comparison program that,for any two sequences in question, generates an alignment havingidentical nucleotide residue matches and an identical percent sequenceidentity when compared to the corresponding alignment generated by GAPVersion 10.

Traits or markers are considered to be linked if they co-segregate. A1/100 probability of recombination per generation is defined as a mapdistance of 1.0 centiMorgan (1.0 cM). Genetic elements or genes locatedon a single chromosome segment are physically linked. Two loci can belocated in close proximity such that recombination between homologouschromosome pairs does not occur between the two loci during meiosis withhigh frequency, e.g., such that linked loci co-segregate at least about90% of the time, e.g., 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%,99.5%, 99.75%, or more of the time. Genetic elements located within achromosome segment are also genetically linked, typically within agenetic recombination distance of less than or equal to 50 centimorgans(cM), e.g., about 49, 40, 30, 20, 10, 5, 4, 3, 2, 1, 0.75, 0.5, or 0.25cM or less. That is, two genetic elements within a single chromosomesegment undergo recombination during meiosis with each other at afrequency of less than or equal to about 50%, e.g., about 49%, 40%, 30%,20%, 10%, 5%, 4%, 3%, 2%, 1%, 0.75%, 0.5%, or 0.25% or less. Closelylinked markers display a cross over frequency with a given marker ofabout 10% or less (the given marker is within about 10 cM of a closelylinked marker). In specific embodiments, a closely linked marker iswithin 10 cM, 9 cM, 8 cM, 7 cM, 6 cM, 5 cM, 4 cM, 3 cM, 2 cM or 1 cM ofany given marker disclosed herein. In further embodiments, a markerassociated with one of the markers disclosed herein can be within 75 Kb,60 Kb, 50 Kb, 40 Kb, 30 Kb, 20K, 10 Kb, 5 Kb or less of the disclosedmarker. Put another way, closely linked loci co-segregate at least about90% of the time. Genetic linkage as evaluated by recombination frequencyis impacted by the chromatin structure of the region comprising theloci. Typically, the region is assumed to have a euchromatin structureduring initial evaluations. However, some regions, such are regionscloser to centrosomes, have a heterochromatin structure. Without furtherinformation, the predicted physical distance between genetic mappositions is based on the assumption that the region is euchromatic,however if the region comprises heterochromatin the markers may bephysically closer together. With regard to physical position on achromosome, closely linked markers can be separated, for example, byabout 1 megabase (Mb; 1 million nucleotides), about 500 kilobases (Kb;1000 nucleotides), about 400 Kb, about 300 Kb, about 200 Kb, about 100Kb, about 50 Kb, about 25 Kb, about 10 Kb, about 5 Kb, about 2 Kb, about1 Kb, about 500 nucleotides, about 250 nucleotides, or less.

When referring to the relationship between two genetic elements, such asa genetic element contributing to resistance and a proximal marker,“coupling” phase linkage indicates the state where the “favorable”allele at the resistance locus is physically associated on the samechromosome strand as the “favorable” allele of the respective linkedmarker locus. In coupling phase, both favorable alleles are inheritedtogether by progeny that inherit that chromosome strand. In “repulsion”phase linkage, the “favorable” allele at the locus of interest (e.g., aQTL for resistance) is physically linked with an “unfavorable” allele atthe proximal marker locus, and the two “favorable” alleles are notinherited together (i.e., the two loci are “out of phase” with eachother).

Markers are used to define a specific locus on the soybean genome. Eachmarker is therefore an indicator of a specific segment of DNA, having aunique nucleotide sequence. Map positions provide a measure of therelative positions of particular markers with respect to one another.When a trait is stated to be linked to a given marker it will beunderstood that the actual DNA segment whose sequence affects the traitgenerally co-segregates with the marker. More precise and definitelocalization of a trait can be obtained if markers are identified onboth sides of the trait. By measuring the appearance of the marker(s) inprogeny of crosses, the existence of the trait can be detected byrelatively simple molecular tests without actually evaluating theappearance of the trait itself, which can be difficult andtime-consuming because the actual evaluation of the trait requiresgrowing plants to a stage and/or under environmental conditions wherethe trait can be expressed. Molecular markers have been widely used todetermine genetic composition in soybeans.

Favorable genotypes associated with at least trait of interest may beidentified by one or more methodologies. In some examples one or moremarkers are used, including but not limited to AFLPs, RFLPs, ASH, SSRs,SNPs, indels, padlock probes, molecular inversion probes, microarrays,sequencing, and the like. In some methods, a target nucleic acid isamplified prior to hybridization with a probe. In other cases, thetarget nucleic acid is not amplified prior to hybridization, such asmethods using molecular inversion probes (see, for example Hardenbol etal. (2003) Nat Biotech 21:673-678). In some examples, the genotyperelated to a specific trait is monitored, while in other examples, agenome-wide evaluation including but not limited to one or more ofmarker panels, library screens, association studies, microarrays, genechips, expression studies, or sequencing such as whole-genomeresequencing and genotyping-by-sequencing (GBS) may be used. In someexamples, no target-specific probe is needed, for example by usingsequencing technologies, including but not limited to next-generationsequencing methods (see, for example, Metzker (2010) Nat Rev Genet.11:31-46; and, Egan et al. (2012) Am J Bot 99:175-185) such assequencing by synthesis (e.g., Roche 454 pyrosequencing, Illumina GenomeAnalyzer, and Ion Torrent PGM or Proton systems), sequencing by ligation(e.g., SOLiD from Applied Biosystems, and Polnator system from AzcoBiotech), and single molecule sequencing (SMS or third-generationsequencing) which eliminate template amplification (e.g., Helicossystem, and PacBio RS system from Pacific BioSciences). Furthertechnologies include optical sequencing systems (e.g., Starlight fromLife Technologies), and nanopore sequencing (e.g., GridION from OxfordNanopore Technologies). Each of these may be coupled with one or moreenrichment strategies for organellar or nuclear genomes in order toreduce the complexity of the genome under investigation via PCR,hybridization, restriction enzyme (see, e.g., Elshire et al. (2011) PLoSONE 6:e19379), and expression methods. In some examples, no referencegenome sequence is needed in order to complete the analysis.

The use of marker assisted selection (MAS) to select a soybean plant orgermplasm which has a certain marker locus, haplotype or marker profileis provided. For instance, in certain examples a soybean plant orgermplasm possessing a certain predetermined favorable marker locus orhaplotype will be selected via MAS. In certain other examples, a soybeanplant or germplasm possessing a certain predetermined favorable markerprofile will be selected via MAS.

Using MAS, soybean plants or germplasm can be selected for markers ormarker alleles that positively correlate with soybean cyst nematoderesistance, without actually raising soybean and measuring forresistance (or, contrawise, soybean plants can be selected against ifthey possess markers that negatively correlate with resistance). MAS isa powerful tool to select for desired phenotypes and for introgressingdesired traits into cultivars of soybean (e.g., introgressing desiredtraits into elite lines). MAS is easily adapted to high throughputmolecular analysis methods that can quickly screen large numbers ofplant or germplasm genetic material for the markers of interest and ismuch more cost effective than raising and observing plants for visibletraits.

In some embodiments, the molecular markers or marker loci are detectedusing a suitable amplification-based detection method. In these types ofmethods, nucleic acid primers are typically hybridized to the conservedregions flanking the polymorphic marker region. In certain methods,nucleic acid probes that bind to the amplified region are also employed.In general, synthetic methods for making oligonucleotides, includingprimers and probes, are well known in the art. For example,oligonucleotides can be synthesized chemically according to the solidphase phosphoramidite triester method described by Beaucage andCaruthers (1981) Tetrahedron Letts 22:1859-1862, e.g., using acommercially available automated synthesizer, e.g., as described inNeedham-VanDevanter, et al. (1984) Nucleic Acids Res. 12:6159-6168.Oligonucleotides, including modified oligonucleotides, can also beordered from a variety of commercial sources known to persons of skillin the art.

It will be appreciated that suitable primers and probes to be used canbe designed using any suitable method. It is not intended that theinvention be limited to any particular primer, primer pair or probe. Forexample, primers can be designed using any suitable software program,such as LASERGENE® or Primer3.

It is not intended that the primers be limited to generating an ampliconof any particular size. For example, the primers used to amplify themarker loci and alleles herein are not limited to amplifying the entireregion of the relevant locus. In some embodiments, marker amplificationproduces an amplicon at least 20 nucleotides in length, oralternatively, at least 50 nucleotides in length, or alternatively, atleast 100 nucleotides in length, or alternatively, at least 200nucleotides in length.

Non-limiting examples of polynucleotide primers useful for detecting themarker loci provided herein are provided in Table 3 and include, forexample, SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69,70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87,88, 89, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112,113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126,127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 140, 141, 144,145, 148, 149, 152, 153, 156, 157, 160, 161, 164, 165, 168, or 169 orvariants or fragments thereof.

PCR, RT-PCR, and LCR are in particularly broad use as amplification andamplification-detection methods for amplifying nucleic acids of interest(e.g., those comprising marker loci), facilitating detection of themarkers. Details regarding the use of these and other amplificationmethods are well known in the art and can be found in any of a varietyof standard texts. Details for these techniques can also be found innumerous journal and patent references, such as Mullis, et al. (1987)U.S. Pat. No. 4,683,202; Arnheim & Levinson (Oct. 1, 1990) C&EN 36-47;Kwoh, et al. (1989) Proc. Natl. Acad. Sci. USA 86:1173; Guatelli, etal., (1990) Proc. Natl. Acad. Sci. USA87:1874; Lomeli, et al., (1989) J.Clin. Chem. 35:1826; Landegren, et al., (1988) Science 241:1077-1080;Van Brunt, (1990) Biotechnology 8:291-294; Wu and Wallace, (1989) Gene4:560; Barringer, et al., (1990) Gene 89:117, and Sooknanan and Malek,(1995) Biotechnology 13:563-564.

Such nucleic acid amplification techniques can be applied to amplifyand/or detect nucleic acids of interest, such as nucleic acidscomprising marker loci. Amplification primers for amplifying usefulmarker loci and suitable probes to detect useful marker loci or togenotype SNP alleles are provided. For example, exemplary primers andprobes are provided in SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29,30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65,66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83,84, 85, 86, 87, 88, 89, 100, 101, 102, 121, 122, 123, 124, 125, 126,127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 140, 141, 144,145, 148, 149, 152, 153, 156, 157, 160, 161, 164, 165, 168, or 169 andin Tables 3 and 4, and the genomic loci comprising the various markerloci provided herein are provided in SEQ ID NOS: 103, 104, 105, 106,107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120,138, 139, 142, 143, 146, 147, 150, 151, 154, 155, 158, 159, 162, 163,166, 167, 170 or 171 and in Table 5. Non-limiting examples of ampliconsequences comprising the marker loci provided herein are provided inTable 6. However, one of skill will immediately recognize that otherprimer and probe sequences could also be used. For instance primers toeither side of the given primers can be used in place of the givenprimers, so long as the primers can amplify a region that includes theallele to be detected, as can primers and probes directed to other SNPmarker loci. Further, it will be appreciated that the precise probe tobe used for detection can vary, e.g., any probe that can identify theregion of a marker amplicon to be detected can be substituted for thoseexamples provided herein. Further, the configuration of theamplification primers and detection probes can, of course, vary. Thus,the compositions and methods are not limited to the primers and probesspecifically recited herein.

In certain examples, probes will possess a detectable label. Anysuitable label can be used with a probe. Detectable labels suitable foruse with nucleic acid probes include, for example, any compositiondetectable by spectroscopic, radioisotopic, photochemical, biochemical,immunochemical, electrical, optical, or chemical means. Useful labelsinclude biotin for staining with labeled streptavidin conjugate,magnetic beads, fluorescent dyes, radiolabels, enzymes, and colorimetriclabels. Other labels include ligands, which bind to antibodies labeledwith fluorophores, chemiluminescent agents, and enzymes. A probe canalso constitute radiolabelled PCR primers that are used to generate aradiolabelled amplicon. Labeling strategies for labeling nucleic acidsand corresponding detection strategies can be found, e.g., in Haugland(1996) Handbook of Fluorescent Probes and Research Chemicals SixthEdition by Molecular Probes, Inc. (Eugene Oreg.); or Haugland (2001)Handbook of Fluorescent Probes and Research Chemicals Eighth Edition byMolecular Probes, Inc. (Eugene Oreg.).

Detectable labels may also include reporter-quencher pairs, such as areemployed in Molecular Beacon and TaqMan™ probes. The reporter may be afluorescent organic dye modified with a suitable linking group forattachment to the oligonucleotide, such as to the terminal 3′ carbon orterminal 5′ carbon. The quencher may also be an organic dye, which mayor may not be fluorescent, depending on the embodiment. Generally,whether the quencher is fluorescent or simply releases the transferredenergy from the reporter by non-radiative decay, the absorption band ofthe quencher should at least substantially overlap the fluorescentemission band of the reporter to optimize the quenching. Non-fluorescentquenchers or dark quenchers typically function by absorbing energy fromexcited reporters, but do not release the energy radiatively.

Selection of appropriate reporter-quencher pairs for particular probesmay be undertaken in accordance with known techniques. Fluorescent anddark quenchers and their relevant optical properties from whichexemplary reporter-quencher pairs may be selected are listed anddescribed, for example, in Berlman, Handbook of Fluorescence Spectra ofAromatic Molecules, 2nd ed., Academic Press, New York, 1971, the contentof which is incorporated herein by reference. Examples of modifyingreporters and quenchers for covalent attachment via common reactivegroups that can be added to an oligonucleotide in the present inventionmay be found, for example, in Haugland, Handbook of Fluorescent Probesand Research Chemicals, Molecular Probes of Eugene, Oreg., 1992, thecontent of which is incorporated herein by reference.

In certain examples, reporter-quencher pairs are selected from xanthenedyes including fluoresceins and rhodamine dyes. Many suitable forms ofthese compounds are available commercially with substituents on thephenyl groups, which can be used as the site for bonding or as thebonding functionality for attachment to an oligonucleotide. Anotheruseful group of fluorescent compounds for use as reporters are thenaphthylamines, having an amino group in the alpha or beta position.Included among such naphthylamino compounds are1-dimethylaminonaphthyl-5 sulfonate, 1-anilino-8-naphthalene sulfonateand 2-p-touidinyl-6-naphthalene sulfonate. Other dyes include3-phenyl-7-isocyanatocoumarin; acridines such as9-isothiocyanatoacridine; N-(p-(2-benzoxazolyl)phenyl)maleimide;benzoxadiazoles; stilbenes; pyrenes and the like. In certain otherexamples, the reporters and quenchers are selected from fluorescein andrhodamine dyes. These dyes and appropriate linking methodologies forattachment to oligonucleotides are well known in the art.

Suitable examples of reporters may be selected from dyes such as SYBRgreen, 5-carboxyfluorescein (5-FAM™ available from Applied Biosystems ofFoster City, Calif.), 6-carboxyfluorescein (6-FAM),tetrachloro-6-carboxyfluorescein (TET),2,7-dimethoxy-4,5-dichloro-6-carboxyfluorescein,hexachloro-6-carboxyfluorescein (HEX),6-carboxy-2′,4,7,7′-tetrachlorofluorescein (6-TET™ available fromApplied Biosystems), carboxy-X-rhodamine (ROX),6-carboxy-4′,5′-dichloro-2′,7′-dimethoxyfluorescein (6-JOE™ availablefrom Applied Biosystems), VIC™ dye products available from MolecularProbes, Inc., NED™ dye products available from Applied Biosystems, andthe like. Suitable examples of quenchers may be selected from6-carboxy-tetramethyl-rhodamine, 4-(4-dimethylaminophenylazo) benzoicacid (DABYL), tetramethylrhodamine (TAMRA), BHQ-0™, BHQ-1™, BHQ-2™, andBHQ-3™, each of which are available from Biosearch Technologies, Inc. ofNovato, Calif., QSY-7™, QSY-9™, QSY-21™ and QSY-35™, each of which areavailable from Molecular Probes, Inc., and the like.

In one aspect, real time PCR or LCR is performed on the amplificationmixtures described herein, e.g., using molecular beacons or TaqMan™probes. A molecular beacon (MB) is an oligonucleotide which, underappropriate hybridization conditions, self-hybridizes to form a stem andloop structure. The MB has a label and a quencher at the termini of theoligonucleotide; thus, under conditions that permit intra-molecularhybridization, the label is typically quenched (or at least altered inits fluorescence) by the quencher. Under conditions where the MB doesnot display intra-molecular hybridization (e.g., when bound to a targetnucleic acid, such as to a region of an amplicon during amplification),the MB label is unquenched. Details regarding standard methods of makingand using MBs are well established in the literature and MBs areavailable from a number of commercial reagent sources. See also, e.g.,Leone, et al., (1995) Molecular beacon probes combined withamplification by NASBA enable homogenous real-time detection of RNA,Nucleic Acids Res. 26:2150-2155; Tyagi and Kramer, (1996) Molecularbeacons: probes that fluoresce upon hybridization, Nature Biotechnology14:303-308; Blok and Kramer, (1997) Amplifiable hybridization probescontaining a molecular switch, Mol Cell Probes 11:187-194; Hsuih. etal., (1997) Novel, ligation-dependent PCR assay for detection ofhepatitis C in serum, J Clin Microbiol 34:501-507; Kostrikis, et al.,(1998) Molecular beacons: spectral genotyping of human alleles, Science279:1228-1229; Sokol, et al., (1998) Real time detection of DNA:RNAhybridization in living cells, Proc. Natl. Acad. Sci. U.S.A.95:11538-11543; Tyagi, et al., (1998) Multicolor molecular beacons forallele discrimination, Nature Biotechnology 16:49-53; Bonnet, et al.(1999) Thermodynamic basis of the chemical specificity of structured DNAprobes, Proc. Natl. Acad. Sci. U.S.A. 96:6171-6176; Fang, et al. (1999)Designing a novel molecular beacon for surface-immobilized DNAhybridization studies, J. Am. Chem. Soc. 121:2921-2922; Marras, et al.,(1999) Multiplex detection of single-nucleotide variation usingmolecular beacons, Genet. Anal. Biomol. Eng. 14:151-156; and Vet, et al.(1999) Multiplex detection of four pathogenic retroviruses usingmolecular beacons, Proc. Natl. Acad. Sci. U.S.A. 96:6394-6399.Additional details regarding MB construction and use is found in thepatent literature, e.g., U.S. Pat. Nos. 5,925,517; 6,150,097; and6,037,130.

Another real-time detection method is the 5′-exonuclease detectionmethod, also called the TaqMan™ assay, as set forth in U.S. Pat. Nos.5,804,375; 5,538,848; 5,487,972; and 5,210,015, each of which is herebyincorporated by reference in its entirety. In the TaqMan™ assay, amodified probe, typically 10-25 nucleic acids in length, is employedduring PCR which binds intermediate to or between the two members of theamplification primer pair. The modified probe possesses a reporter and aquencher and is designed to generate a detectable signal to indicatethat it has hybridized with the target nucleic acid sequence during PCR.As long as both the reporter and the quencher are on the probe, thequencher stops the reporter from emitting a detectable signal. However,as the polymerase extends the primer during amplification, the intrinsic5′ to 3′ nuclease activity of the polymerase degrades the probe,separating the reporter from the quencher, and enabling the detectablesignal to be emitted. Generally, the amount of detectable signalgenerated during the amplification cycle is proportional to the amountof product generated in each cycle.

It is well known that the efficiency of quenching is a strong functionof the proximity of the reporter and the quencher, i.e., as the twomolecules get closer, the quenching efficiency increases. As quenchingis strongly dependent on the physical proximity of the reporter andquencher, the reporter and the quencher are preferably attached to theprobe within a few nucleotides of one another, usually within 30nucleotides of one another, more preferably with a separation of fromabout 6 to 16 nucleotides. Typically, this separation is achieved byattaching one member of a reporter-quencher pair to the 5′ end of theprobe and the other member to a nucleotide about 6 to 16 nucleotidesaway, in some cases at the 3′ end of the probe.

Separate detection probes can also be omitted in amplification/detectionmethods, e.g., by performing a real time amplification reaction thatdetects product formation by modification of the relevant amplificationprimer upon incorporation into a product, incorporation of labelednucleotides into an amplicon, or by monitoring changes in molecularrotation properties of amplicons as compared to unamplified precursors(e.g., by fluorescence polarization).

Further, it will be appreciated that amplification is not a requirementfor marker detection—for example, one can directly detect unamplifiedgenomic DNA simply by performing a Southern blot on a sample of genomicDNA. Procedures for performing Southern blotting, amplification e.g.,(PCR, LCR, or the like), and many other nucleic acid detection methodsare well established and are taught, e.g., in Sambrook, et al.,Molecular Cloning—A Laboratory Manual (3d ed.), Vol. 1-3, Cold SpringHarbor Laboratory, Cold Spring Harbor, N.Y., 2000 (“Sambrook”); CurrentProtocols in Molecular Biology, F. M. Ausubel, et al., eds., CurrentProtocols, a joint venture between Greene Publishing Associates, Inc.and John Wiley & Sons, Inc., (supplemented through 2002) (“Ausubel”))and PCR Protocols A Guide to Methods and Applications (Innis, et al.,eds) Academic Press Inc. San Diego, Calif. (1990) (Innis). Additionaldetails regarding detection of nucleic acids in plants can also befound, e.g., in Plant Molecular Biology (1993) Croy (ed.) BIOSScientific Publishers, Inc.

Other techniques for detecting SNPs can also be employed, such as allelespecific hybridization (ASH). ASH technology is based on the stableannealing of a short, single-stranded, oligonucleotide probe to acompletely complementary single-stranded target nucleic acid. Detectionis via an isotopic or non-isotopic label attached to the probe. For eachpolymorphism, two or more different ASH probes are designed to haveidentical DNA sequences except at the polymorphic nucleotides. Eachprobe will have exact homology with one allele sequence so that therange of probes can distinguish all the known alternative allelesequences. Each probe is hybridized to the target DNA. With appropriateprobe design and hybridization conditions, a single-base mismatchbetween the probe and target DNA will prevent hybridization.

Real-time amplification assays, including MB or TaqMan™ based assays,are especially useful for detecting SNP alleles. In such cases, probesare typically designed to bind to the amplicon region that includes theSNP locus, with one allele-specific probe being designed for eachpossible SNP allele. For instance, if there are two known SNP allelesfor a particular SNP locus, “A” or “C,” then one probe is designed withan “A” at the SNP position, while a separate probe is designed with a“C” at the SNP position. While the probes are typically identical to oneanother other than at the SNP position, they need not be. For instance,the two allele-specific probes could be shifted upstream or downstreamrelative to one another by one or more bases. However, if the probes arenot otherwise identical, they should be designed such that they bindwith approximately equal efficiencies, which can be accomplished bydesigning under a strict set of parameters that restrict the chemicalproperties of the probes. Further, a different detectable label, forinstance a different reporter-quencher pair, is typically employed oneach different allele-specific probe to permit differential detection ofeach probe. In certain examples, each allele-specific probe for acertain SNP locus is 11-20 nucleotides in length, dual-labeled with aflorescence quencher at the 3′ end and either the 6-FAM(6-carboxyfluorescein) or VIC(4,7,2′-trichloro-7′-phenyl-6-carboxyfluorescein) fluorophore at the 5′end.

To effectuate SNP allele detection, a real-time PCR reaction can beperformed using primers that amplify the region including the SNP locus,for instance the sequences listed in Table 5, the reaction beingperformed in the presence of all allele-specific probes for the givenSNP locus. By then detecting signal for each detectable label employedand determining which detectable label(s) demonstrated an increasedsignal, a determination can be made of which allele-specific probe(s)bound to the amplicon and, thus, which SNP allele(s) the ampliconpossessed. For instance, when 6-FAM- and VIC-labeled probes areemployed, the distinct emission wavelengths of 6-FAM (518 nm) and VIC(554 nm) can be captured. A sample that is homozygous for one allelewill have fluorescence from only the respective 6-FAM or VICfluorophore, while a sample that is heterozygous at the analyzed locuswill have both 6-FAM and VIC fluorescence.

The KASPar® and Illumina® Detection Systems are additional examples ofcommercially-available marker detection systems. KASPar® is ahomogeneous fluorescent genotyping system which utilizes allele specifichybridization and a unique form of allele specific PCR (primerextension) in order to identify genetic markers (e.g. a particular SNPlocus associated with soybean cyst nematode resistance). Illumina®detection systems utilize similar technology in a fixed platform format.The fixed platform utilizes a physical plate that can be created with upto 384 markers. The Illumina® system is created with a single set ofmarkers that cannot be changed and utilizes dyes to indicate markerdetection.

These systems and methods represent a wide variety of availabledetection methods which can be utilized to detect markers associatedwith improved resistance to soybean cyst nematode, but any othersuitable method could also be used.

Introgression of soybean cyst nematode resistance into non-resistant orless-resistant soybean germplasm is provided. Any method forintrogressing one or more marker loci into soybean plants known to oneof skill in the art can be used. Typically, a first soybean germplasmthat contains soybean cyst nematode resistance derived from a particularmarker locus, haplotype or marker profile and a second soybean germplasmthat lacks such resistance derived from the marker locus, haplotype ormarker profile are provided. The first soybean germplasm may be crossedwith the second soybean germplasm to provide progeny soybean germplasm.These progeny germplasm are screened to determine the presence ofsoybean cyst nematode resistance derived from the marker locus,haplotype or marker profile, and progeny that tests positive for thepresence of resistance derived from the marker locus, haplotype ormarker profile are selected as being soybean germplasm into which themarker locus, haplotype or marker profile has been introgressed. Methodsfor performing such screening are well known in the art and any suitablemethod can be used.

One application of MAS is to use the resistance markers, haplotypes ormarker profiles to increase the efficiency of an introgression orbackcrossing effort aimed at introducing a resistance trait into adesired (typically high yielding) background. In marker assistedbackcrossing of specific markers from a donor source, e.g., to an elitegenetic background, one selects among backcross progeny for the donortrait and then uses repeated backcrossing to the elite line toreconstitute as much of the elite background's genome as possible.

Thus, the markers and methods can be utilized to guide marker assistedselection or breeding of soybean varieties with the desired complement(set) of allelic forms of chromosome segments associated with superioragronomic performance (resistance, along with any other availablemarkers for yield, disease tolerance, etc.). Any of the disclosed markerloci, marker alleles, haplotypes, or marker profiles can be introducedinto a soybean line via introgression, by traditional breeding (orintroduced via transformation, or both) to yield a soybean plant withsuperior agronomic performance. The number of alleles associated withresistance that can be introduced or be present in a soybean plantranges from 1 to the number of alleles disclosed herein, each integer ofwhich is incorporated herein as if explicitly recited.

The markers and methods provided herein can also be utilized to guidemarker assisted selection or breeding of soybean varieties comprisingother soybean cyst nematode resistance markers or alleles to create amolecular stack for soybean cyst nematode resistance. For example, anyof the marker loci provided herein can be introduced into a soybean linehaving one or more of the soybean cyst nematode resistance loci rhg1,rhg2, rhg3 or rhg5. In one embodiment, any one or more of the markerloci provided herein can be stacked with the rhg1 locus. In anotherembodiment, any one or more of the marker loci provided herein can bestacked with the rhg2 locus. In a further embodiment, any one or more ofthe marker loci provided herein can be stacked with the rhg1 and rhg2loci.

This also provides a method of making a progeny soybean plant and theseprogeny soybean plants, per se. The method comprises crossing a firstparent soybean plant with a second soybean plant and growing the femalesoybean plant under plant growth conditions to yield soybean plantprogeny. Methods of crossing and growing soybean plants are well withinthe ability of those of ordinary skill in the art. Such soybean plantprogeny can be assayed for alleles associated with resistance and,thereby, the desired progeny selected. Such progeny plants or seed canbe sold commercially for soybean production, used for food, processed toobtain a desired constituent of the soybean, or further utilized insubsequent rounds of breeding. At least one of the first or secondsoybean plants is a soybean plant in that it comprises at least one ofthe marker loci or marker profiles, such that the progeny are capable ofinheriting the marker locus or marker profile.

Often, a method is applied to at least one related soybean plant such asfrom progenitor or descendant lines in the subject soybean plantspedigree such that inheritance of the desired resistance can be traced.The number of generations separating the soybean plants being subject tothe methods provided herein will generally be from 1 to 20, commonly 1to 5, and typically 1, 2, or 3 generations of separation, and quiteoften a direct descendant or parent of the soybean plant will be subjectto the method (i.e., 1 generation of separation).

Genetic diversity is important for long term genetic gain in anybreeding program. With limited diversity, genetic gain will eventuallyplateau when all of the favorable alleles have been fixed within theelite population. One objective is to incorporate diversity into anelite pool without losing the genetic gain that has already been madeand with the minimum possible investment. MAS provides an indication ofwhich genomic regions and which favorable alleles from the originalancestors have been selected for and conserved over time, facilitatingefforts to incorporate favorable variation from exotic germplasm sources(parents that are unrelated to the elite gene pool) in the hopes offinding favorable alleles that do not currently exist in the elite genepool.

For example, the markers, haplotypes, primers, probes, and markerprofiles can be used for MAS in crosses involving elite×exotic soybeanlines by subjecting the segregating progeny to MAS to maintain majoryield alleles, along with the resistance marker alleles herein.

As an alternative to standard breeding methods of introducing traits ofinterest into soybean (e.g., introgression), transgenic approaches canalso be used to create transgenic plants with the desired traits. Inthese methods, exogenous nucleic acids that encode a desired markerloci, marker profile or haplotype are introduced into target plants orgermplasm. For example, a nucleic acid that codes for a resistance traitis cloned, e.g., via positional cloning, and introduced into a targetplant or germplasm.

Experienced plant breeders can recognize resistant soybean plants in thefield, and can select the resistant individuals or populations forbreeding purposes or for propagation. In this context, the plant breederrecognizes “resistant” and “non-resistant” or “susceptible” soybeanplants. However, plant resistance is a phenotypic spectrum consisting ofextremes in resistance and susceptibility, as well as a continuum ofintermediate resistance phenotypes. Evaluation of these intermediatephenotypes using reproducible assays are of value to scientists who seekto identify genetic loci that impart resistance, to conduct markerassisted selection for resistant populations, and to use introgressiontechniques to breed a resistance trait into an elite soybean line, forexample.

By “improved resistance” is intended that the plants show a decrease inthe disease symptoms that are the outcome of plant exposure to soybeancyst nematode. That is, the damage caused by soybean cyst nematode isprevented, or alternatively, the disease symptoms caused by soybean cystnematode is minimized or lessened. Thus, improved resistance to soybeancyst nematode can result in reduction of the disease symptoms by atleast about 2% to at least about 6%, at least about 5% to about 50%, atleast about 10% to about 60%, at least about 30% to about 70%, at leastabout 40% to about 80%, or at least about 50% to about 90% or greater.Hence, the methods provided herein can be utilized to protect plantsfrom soybean cyst nematode.

Screening and selection of soybean cyst nematode resistant soybeanplants may be performed, for example, by exposing plants to soybean cystnematode and selecting those plants showing resistance to soybean cystnematode. Various assays can be used to measure resistance or improvedresistance to soybean cyst nematode. For example, soybean cyst nematoderesistance can be determined by visual observations after plant exposureto a particular race of soybean cyst nematode, such as race 1, 2, 3, 5or 14. Scores range from 1 to 9 and indicate visual observations ofresistance as compared to other genotypes in the test. A score of 1indicates soybean cyst nematode are able to infect the plant and causeyield loss, while a score of 9 indicates soybean cyst nematoderesistance. Preliminary scores are reported as double digits, forexample, ‘55’ indicates a preliminary score of 5 on the scale of 1 to 9.

Non-limiting examples of soybean cyst nematode resistance phenotypicscreening are described in detail below.

Multiple populations of Heterodera glycines are maintained and increasedon host plants. These populations are used to identify, purify, andcharacterize elite soybean varieties for resistance to soybean cystnematode. The following races of soybean cyst nematode are maintained:Race 1 (Type HG 2.5), Race 2 (Type HG 1.2.5.7), Race 3 (Type HG 0 orType HG 7), Race 5 (Type HG 2.5.7), and Race 14 (Type HG 1.3.6.7).

Eggs or second stage juveniles (J2) are used to inoculate host plants toincrease their population. Soybean cyst nematode infestation requires aminimum 35 days before the cysts reach maturity and can be used toinoculate soybean experiments. Cyst eggs/J2 inoculant is harvestedthrough a series of washings, grindings, and screenings. Screens areused progressing from larger to smaller sizes, ending with a #500 (25μm) screen.

Soybean plants are grown in cones. Cones are long containersapproximately 12 inches long and 1.5 inches in diameter at the top(e.g., Ray Leach Cone-Tainers™). The cone is designed to easily removethe root mass. Three to seven days after planting, an inoculum channelis made in the cone containing the experimental line by poking a 4 inchhole with a 10 ml pipette tip. One ml of inoculum is dispensed into thechannel. The plants are watered manually for the duration of the test,with watering being moderately light during the first 3-5 days until J2infects the roots.

Plants are scored approximately 28-35 days following inoculation whencyst reproduction on susceptible checks is sufficiently high. Plants areremoved from their cones and the soil is removed from the roots bygently dipping the roots into a bucket of water. The plants are screenedto identify native resistance to one or more of the five races ofsoybean cyst nematode inoculated using a combination of three methods(1) visual 9-6-1 score; (2) visual full count; and/or (3) microscopecount score depending on the stage of the line when screened. Ingeneral, lines earlier in the development cycle (R1-R2) are screened bythe visual 9-6-1 method, and lines that have progressed to laterdevelopment phases (R3-R5) are screened by the visual full count and/ormicroscope count method(s).

One typical phenotyping method is a visual evaluation of the roots.Susceptible checks are first evaluated for the development of cysts onthe root system. These counts are recorded and averaged across theexperiment to determine the susceptible (SUS) check average. Roots fromthe test plants are then scored based on a comparison with the averageof the susceptible checks as follows:

9=0-15% of the susceptible checks average

6=16-40% of the susceptible checks average

1=≧41% of the susceptible checks average

Visual Counts:

In this method, known checks are counted and reported in full. Observedcysts on the test plants are counted for comparison to the susceptiblecheck plant scores. Cyst counts are converted to 1-9 scores based on thefemale index (FI). The female index (FI) is the percentage of the numberof females cysts produced on each experimental line divided by thenumber produced on a standard susceptible soybean check, then the resultis multiplied by 100. A low FI (<10) means that the soybean cystnematode population is not able to reproduce well on the test line, ahigh FI means that the soybean cyst nematode population is able toreproduce well on the test line.

Microscope Counts:

Cysts counts for soybean cyst nematode assays for checks andexperimental line are determined by washing cysts from roots andcounting the number of cysts under the microscope.

At about 28-35 days after inoculation, roots from the susceptible checkcontrols are examined for yellow cysts to assess whether to begin theprocess of evaluating the test. Experimental lines are compared withknown standard checks. Once adequate levels of cysts are detected on thecheck varieties, plants from the test lines are removed from cones oneat a time. Soil is removed from roots by gently dipping the roots into abucket of water. The root tissue is placed on a 850 micron (#20) poresieve stacked over a 250 micron (#60) pore sieve and sprayed with a jetof water to dislodge cysts from the roots. Collected cysts are rinsedfrom the #60 sieve into a clean labeled cup using no more than 30 mls ofadditional water.

Once all the samples are collected, each sample is counted using agridded counting dish under a stereo microscope. The number of cystscounted are recorded for each sample. Cyst counts on the test plants areconverted to the 1-9 scoring scale based on the female index (FI)described above.

The following exemplary soybean cyst nematode checks can be planted andused to monitor cyst development:

TABLE 7 Exemplary soybean cyst nematode checks. Race 1 Race 2 Race 3Race 5 Race 14 92B12 RES 95M60 RES 9182 RES 92B12 RES 9182 RES 9281 SUS9281 SUS 9281 SUS 9281 SUS 9281 SUS 9234 RES PI437654 RES 9234 RES 9234RES 9234 SUS 9392 SUS 9392 SUS 9392 SUS 9392 SUS 9392 SUS 91M12 MR 9234MR 93B15 MR 91M12 SUS 93B15 MR RES = Resistant; SUS = Susceptible; and,MR = Moderately Resistant

In some examples, a kit or an automated system for detecting markerloci, haplotypes, and marker profiles, and/or correlating the markerloci, haplotypes, and marker profiles with a desired phenotype (e.g.,soybean cyst nematode resistance) are provided. As used herein, “kit”refers to a set of reagents for the purpose of performing the variousmethods of detecting or identifying herein, more particularly, theidentification and/or the detection of a soybean plant or germplasmhaving improved resistance to soybean cyst nematode.

In one embodiment, a kit for detecting or selecting at least one soybeanplant or soybean germplasm with improved resistance to soybean cystnematode is provided. Such a kit comprises (a) primers or probes fordetecting one or more marker loci associated with resistance to soybeancyst nematode, wherein at least one of the primers and probes in the kitare capable of detecting a marker locus comprising one or more ofS08271-1-Q2, P7659A-2, S08051-1-Q1, S07158-1-Q1, S07159-1-Q1,S06818-3-Q2, S06820-1-Q3, S06821-1-Q2, S16001-001-Q001 or a markerclosely linked thereto on linkage group G; and, (b) instructions forusing the primers or probes for detecting the one or more marker lociand correlating the detected marker loci with predicted resistance tosoybean cyst nematode.

Thus, a typical kit or system can include a set of marker probes orprimers configured to detect at least one favorable allele of one ormore marker loci associated with resistance to soybean cyst nematode,for instance a favorable marker locus, haplotype or marker profile.These probes or primers can be configured, for example, to detect themarker loci noted in the tables and examples herein, e.g., using anyavailable allele detection format, such as solid or liquid phase arraybased detection, microfluidic-based sample detection, etc. The systemsand kits can further include packaging materials for packaging theprobes, primers, or instructions, controls such as control amplificationreactions that include probes, primers or template nucleic acids foramplifications, molecular size markers, or the like.

A typical system can also include a detector that is configured todetect one or more signal outputs from the set of marker probes orprimers, or amplicon thereof, thereby identifying the presence orabsence of the allele. A wide variety of signal detection apparatus areavailable, including photo multiplier tubes, spectrophotometers, CCDarrays, scanning detectors, phototubes and photodiodes, microscopestations, galvo-scans, microfluidic nucleic acid amplification detectionappliances and the like. The precise configuration of the detector willdepend, in part, on the type of label used to detect the marker allele,as well as the instrumentation that is most conveniently obtained forthe user. Detectors that detect fluorescence, phosphorescence,radioactivity, pH, charge, absorbance, luminescence, temperature,magnetism or the like can be used. Typical detector examples includelight (e.g., fluorescence) detectors or radioactivity detectors. Forexample, detection of a light emission (e.g., a fluorescence emission)or other probe label is indicative of the presence or absence of amarker allele. Fluorescent detection is generally used for detection ofamplified nucleic acids (however, upstream and/or downstream operationscan also be performed on amplicons, which can involve other detectionmethods). In general, the detector detects one or more label (e.g.,light) emission from a probe label, which is indicative of the presenceor absence of a marker allele. The detector(s) optionally monitors oneor a plurality of signals from an amplification reaction. For example,the detector can monitor optical signals which correspond to “real time”amplification assay results.

System or kit instructions that describe how to use the system or kit orthat correlate the presence or absence of the favorable allele with thepredicted resistance are also provided. For example, the instructionscan include at least one look-up table that includes a correlationbetween the presence or absence of the favorable alleles, haplotypes, ormarker profiles and the predicted resistance. The precise form of theinstructions can vary depending on the components of the system, e.g.,they can be present as system software in one or more integrated unit ofthe system (e.g., a microprocessor, computer or computer readablemedium), or can be present in one or more units (e.g., computers orcomputer readable media) operably coupled to the detector. As noted, inone typical example, the system instructions include at least onelook-up table that includes a correlation between the presence orabsence of the favorable alleles and predicted resistance. Theinstructions also typically include instructions providing a userinterface with the system, e.g., to permit a user to view results of asample analysis and to input parameters into the system.

Isolated polynucleotides comprising the nucleic acid sequences of theprimers and probes provided herein are also encompassed herein. In oneembodiment, the isolated polynucleotide comprises a polynucleotidecapable of detecting a marker locus of the soybean genome comprising amarker locus comprising one or more of S08271-1-Q2, P7659A-2,S08051-1-Q1, S07158-1-Q1, S07159-1-Q1, S06818-3-Q2, S06820-1-Q3,S06821-1-Q2, S16001-001-Q001 or a marker closely linked thereto onlinkage group G.

In specific embodiments, the isolated polynucleotide comprises: (a) apolynucleotide comprising SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29,30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65,66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83,84, 85, 86, 87, 88, 89, 100, 101, 102, 103, 104, 105, 106, 107, 108,109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122,123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136,137, 140, 141, 144, 145, 148, 149, 152, 153, 156, 157, 160, 161, 164,165, 168, 169, 138, 139, 142, 143, 146, 147, 150, 151, 154, 155, 158,159, 162, 163, 166, 167, 170 or 171; (b) a polynucleotide having atleast 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%sequence identity to SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30,31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48,49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66,67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84,85, 86, 87, 88, 89, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109,110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123,124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137,140, 141, 144, 145, 148, 149, 152, 153, 156, 157, 160, 161, 164, 165,168, or 169, 138, 139, 142, 143, 146, 147, 150, 151, 154, 155, 158, 159,162, 163, 166, 167, 170 or 171; or (c) a polynucleotide comprising atleast 10 contiguous nucleotides of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8,9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26,27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44,45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62,63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80,81, 82, 83, 84, 85, 86, 87, 88, 89, 100, 101, 102, 103, 104, 105, 106,107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120,121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134,135, 136, 137, 140, 141, 144, 145, 148, 149, 152, 153, 156, 157, 160,161, 164, 165, 168, 169, 138, 139, 142, 143, 146, 147, 150, 151, 154,155, 158, 159, 162, 163, 166, 167, 170 or 171.

In certain embodiments, the isolated nucleic acids are capable ofhybridizing under stringent conditions to nucleic acids of a soybeancultivar resistant to soybean cyst nematode, for instance to particularSNPs that comprise a marker locus, haplotype or marker profile.

As used herein, a substantially identical or complementary sequence is apolynucleotide that will specifically hybridize to the complement of thenucleic acid molecule to which it is being compared under highstringency conditions. A polynucleotide is said to be the “complement”of another polynucleotide if they exhibit complementarity. As usedherein, molecules are said to exhibit “complete complementarity” whenevery nucleotide of one of the polynucleotide molecules is complementaryto a nucleotide of the other. Two molecules are said to be “minimallycomplementary” if they can hybridize to one another with sufficientstability to permit them to remain annealed to one another under atleast conventional “low-stringency” conditions. Similarly, the moleculesare said to be “complementary” if they can hybridize to one another withsufficient stability to permit them to remain annealed to one anotherunder conventional “high-stringency” conditions.

Appropriate stringency conditions which promote DNA hybridization, forexample, 6× sodium chloride/sodium citrate (SSC) at about 45° C.,followed by a wash of 2×SSC at 50° C., are known to those skilled in theart or can be found in Current Protocols in Molecular Biology, JohnWiley & Sons, N.Y. (1989), 6.3.1-6.3.6. Typically, stringent conditionsfor hybridization and detection will be those in which the saltconcentration is less than about 1.5 M Na ion, typically about 0.01 to1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3 and thetemperature is at least about 30° C. for short probes (e.g., 10 to 50nucleotides) and at least about 60° C. for long probes (e.g., greaterthan 50 nucleotides). Stringent conditions may also be achieved with theaddition of destabilizing agents such as formamide. Exemplary lowstringency conditions include hybridization with a buffer solution of 30to 35% formamide, 1 M NaCl, 1% SDS (sodium dodecyl sulphate) at 37° C.,and a wash in 1× to 2×SSC (20×SSC=3.0 M NaCl/0.3 M trisodium citrate) at50 to 55° C. Exemplary moderate stringency conditions includehybridization in 40 to 45% formamide, 1.0 M NaCl, 1% SDS at 37° C., anda wash in 0.5× to 1×SSC at 55 to 60° C. Exemplary high stringencyconditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at37° C., and a wash in 0.1×SSC at 60 to 65° C. Optionally, wash buffersmay comprise about 0.1% to about 1% SDS. Duration of hybridization isgenerally less than about 24 hours, usually about 4 to about 12 hours.The duration of the wash time will be at least a length of timesufficient to reach equilibrium.

Non-limiting examples of the methods and compositions disclosed hereinare as follows:

1. A method of identifying a first soybean plant or a first soybeangermplasm that displays improved resistance to soybean cyst nematode,the method comprising detecting in the genome of said first soybeanplant or in the genome of said first soybean germplasm at least onemarker locus that is associated with the resistance, wherein:

(a) the at least one marker locus comprises S08271-1-Q2 or a markerclosely linked thereto on linkage group G;

(b) the at least one marker locus comprises P7659A-2 or a marker closelylinked thereto on linkage group G;

(c) the at least one marker locus comprises S08051-1-Q1 or a markerclosely linked thereto on linkage group G;

(d) the at least one marker locus comprises S07158-1-Q1 or a markerclosely linked thereto on linkage group G;

(e) the at least one marker locus comprises S07159-1-Q1 or a markerclosely linked thereto on linkage group G;

(f) the at least one marker locus comprises S06818-3-Q2 or a markerclosely linked thereto on linkage group G;

(g) the at least one marker locus comprises S06820-1-Q3 or a markerclosely linked thereto on linkage group G;

(h) the at least one marker locus comprises S06821-1-Q2 or a markerclosely linked thereto on linkage group G;

(i) the at least one marker locus comprises S16001-001-Q001 or a markerclosely linked thereto on linkage group G;

(j) the at least one marker locus is between about marker Satt309 andBARC-012285-01798 on linkage group G;

(k) the at least one marker locus is between about markerBARC-015371-01813 and BARCSOYSSR_(—)18_(—)0093 on linkage group G;

(l) the at least one marker locus is between about markerBARC-030055-06792 and BARC-025777-05064 on linkage group G;

(m) the at least one marker locus is between about markerBARC-015371-01813 and BARCSOYSSR_(—)18_(—)0093 on linkage group G;

(n) the at least one marker locus is between about markerBARC-015371-01813 and BARCSOYSSR_(—)18_(—)0093 on linkage group G; or

(o) the at least one marker locus comprises at least one of Gm18:926125;Gm18:1138152; Gm18:1517146; Gm18:1518206; Gm18:1520624; Gm18:1520675;Gm18:1520743; Gm18:1524498; Gm18:1548716; Gm18:1550153; Gm18:1550231;Gm18:1552799; Gm18:1554392; Gm18:1554570; Gm18:1554604; Gm18:1554689;Gm18:1555210; Gm18:1560043; Gm18:1560088; Gm18:1560390; Gm18:1560442;Gm18:1560784; Gm18:1561009; Gm18:1561190; Gm18:1561429; Gm18:1561725;Gm18:1562884; Gm18:1563153; Gm18:1564092; Gm18:1565225; Gm18:1565646;Gm18:1566882; Gm18:1567685; Gm18:1567843; Gm18:1568490; Gm18:1568999;Gm18:1569035; Gm18:1569146; Gm18:1570660; Gm18:1572368; Gm18:1577559;Gm18:1578727; Gm18:1579201; Gm18:1579270; Gm18:1579707; Gm18:1579708;Gm18:1581688; Gm18:1583772; Gm18:1584054; Gm18:1584659; Gm18:1589032;Gm18:1595321; Gm18:1598101; Gm18:1599717; Gm18:1599752; Gm18:1599841;Gm18:1600011; Gm18:1600033; Gm18:1600179; Gm18:1601192; Gm18:1601614;Gm18:1602244; Gm18:1603722; Gm18:1604031; Gm18:1605443; Gm18:1606442;Gm18:1606566; Gm18:1606647; Gm18:1609397; Gm18:1610935; Gm18:1612466;Gm18:1612553; Gm18:1614300; Gm18:1614960 Gm18:1618118; Gm18:1626263;Gm18:1626278; Gm18:1627202; Gm18:1627204; Gm18:1629930; Gm18:1634611;Gm18:1643225; Gm18:1653887; Gm18:1654681; Gm18:1654687; Gm18:1657025;Gm18:1680507; Gm18:1700832; Gm18:1700885; Gm18:1701854; Gm18:1702482;Gm18:1702563; Gm18:1702741; Gm18:1703321; Gm18:1706708; Gm18:1706842;Gm18:1707082; Gm18:1707115; Gm18:1707377; Gm18:1708549; Gm18:1717352;Gm18:1721829; Gm18:1723649; Gm18:1723650; Gm18:1724082; Gm18:172553;Gm18:1725630; Gm18:1725815; Gm18:1725932; Gm18:1725991; Gm18:1726068;Gm18:1727330; Gm18:1727343; Gm18:1727903; Gm18:1728146; Gm18:1728824;Gm18:1729347 Gm18:1729673; Gm18:1729866; Gm18:1730855; Gm18:1731068;Gm18:1731184; Gm18:1731725; Gm18:1731938; Gm18:1734691; Gm18:1735510;Gm18:1740118; Gm18:1747766; Gm18:1751156; Gm18:1752808; Gm18:1754310;Gm18:1754895; Gm18:1759167; Gm18:1759307; Gm18:1761263; Gm18:1762686;Gm18:1763519; Gm18:1768783; Gm18:1768805; Gm18:1769619; Gm18:1773903;Gm18:1773911; Gm18:1778021; Gm18:1783028; Gm18:1783194; Gm18:1783357;Gm18:1785320; Gm18:1787549; Gm18:1789215; Gm18:1789352; Gm18:1789553;Gm18:1789934; Gm18:1805509; Gm18:1859739; Gm18:1863987; Gm18:1864738;Gm18:1877951; Gm18:1881755; Gm18:1607524; Gm18:1888247; Gm18:1845911;Gm18:1846008; Gm18:1565826; or Gm18:1918014; or a marker closely linkedthereto on linkage group G.

2. The method of embodiment 2, wherein at least two marker loci aredetected.3. The method of embodiment 2, wherein the at least two marker locicomprise a haplotype that is associated with said resistance.4. The method of embodiment 2, wherein the at least two marker locicomprise a marker profile that is associated with said resistance.5. The method of any one of embodiments 1-4, wherein the germplasm is asoybean variety.6. The method of any one of embodiments 1-5, wherein the method furthercomprises selecting the first soybean plant or first soybean germplasmor a progeny thereof having the at least one marker locus.7. The method of embodiment 6, further comprising crossing the selectedfirst soybean plant or first soybean germplasm with a second soybeanplant or second soybean germplasm.8. The method of embodiment 7, wherein the second soybean plant orsecond soybean germplasm comprises an exotic soybean strain or an elitesoybean strain.9. The method of any one of embodiments 1-8, wherein the detectingcomprises amplifying at least one of said marker loci and detecting theresulting amplified marker amplicon.10. The method of embodiment 9, wherein the amplifying comprises:

a) admixing an amplification primer or amplification primer pair foreach marker locus being amplified with a nucleic acid isolated from thefirst soybean plant or the first soybean germplasm, wherein the primeror primer pair is complementary or partially complementary to a variantor fragment of the genomic locus comprising the marker locus, and iscapable of initiating DNA polymerization by a DNA polymerase using thesoybean nucleic acid as a template; and

b) extending the primer or primer pair in a DNA polymerization reactioncomprising a DNA polymerase and a template nucleic acid to generate atleast one amplicon.

11. The method of embodiment 10, wherein said method comprisesamplifying a variant or fragment of one or more polynucleotidescomprising SEQ ID NOs: 103, 104, 105, 106, 107, 108, 109, 110, 111, 112,113, 114, 115, 116, 117, 118, 119, 120, 138, 139, 142, 143, 146, 147,150, 151, 154, 155, 158, 159, 162, 163, 166, 167, 170 or 171.12. The method of embodiment 10, wherein said primer or primer paircomprises a variant or fragment of one or more polynucleotidescomprising SEQ ID NOs: 103, 104, 105, 106, 107, 108, 109, 110, 111, 112,113, 114, 115, 116, 117, 118, 119, 120, 138, 139, 142, 143, 146, 147,150, 151, 154, 155, 158, 159, 162, 163, 166, 167, 170 or 171.13. The method of embodiment 10, wherein said primer or primer paircomprises a nucleic acid sequence comprising SEQ ID NOs: 1, 2, 3, 4, 5,6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42,43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60,61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,79, 80, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 136, 137,140, 141, 144, 145, 148, 149, 152, 153, 156, 157, 160, 161, 164, 165,168, or 169 or variants or fragments thereof.14. The method of embodiment 10, wherein said primer pair comprises:

a) SEQ ID NOS: 81 and 82; b) SEQ ID NOS: 87 and 88; c) SEQ ID NOS: 89and 90; d) SEQ ID NOS: 91 and 92; e) SEQ ID NOS: 93 and 94; f) SEQ IDNOS:95 and 96; g) SEQ ID NOS: 97 and 98; h) SEQ ID NOS: 99 and 100; i)SEQ ID NOS: 101 and 102; j) SEQ ID NOS: 121 and 122; k) SEQ ID NOS: 121and 123; l) SEQ ID NOS: 124 and 125; m) SEQ ID NOS: 126 and 127; n) SEQID NOS: 128 and 129; o) SEQ ID NOS: 130 and 131; p) SEQ ID NOS: 136 and137; q) SEQ ID NOS: 140 and 141; r) SEQ ID NOS: 144 and 145; s) SEQ IDNOS: 148 and 149; t) SEQ ID NOS: 152 and 153; u) SEQ ID NOS: 156 and157; v) SEQ ID NOS: 160 and 161; w) SEQ ID NOS: 164 and 165; or, x) SEQID NOS: 168 and 169.

15. The method of embodiment 10, wherein the method further comprisesproviding one or more labeled nucleic acid probes suitable for detectionof each marker locus being amplified.16. The method of embodiment 15, wherein said labeled nucleic acid probecomprises a nucleic acid sequence comprising a variant or fragment ofone or more polynucleotides comprising SEQ ID NOs: 103, 104, 105, 106,107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120,138, 139, 142, 143, 146, 147, 150, 151, 154, 155, 158, 159, 162, 163,166, 167, 170 or 171 or complements thereof.17. The method of embodiment 15, wherein the labeled nucleic acid probecomprises a nucleic acid sequence comprising SEQ ID NOs: 81, 82, 83, 84,85, 86, 87, 88, 89, 100, 101, 102, 132, 133, 134, or 135.18. The method of any one of embodiments 1-19, wherein the detectingcomprises DNA sequencing of at least one of said marker loci.19. An isolated polynucleotide capable of detecting a marker locus ofthe soybean genome comprising

(a) the at least one marker locus comprises S08271-1-Q2 or a markerclosely linked thereto on linkage group G;

(b) the at least one marker locus comprises P7659A-2 or a marker closelylinked thereto on linkage group G;

(c) the at least one marker locus comprises S08051-1-Q1 or a markerclosely linked thereto on linkage group G;

(d) the at least one marker locus comprises 507158-1-Q1 or a markerclosely linked thereto on linkage group G;

(e) the at least one marker locus comprises S07159-1-Q1 or a markerclosely linked thereto on linkage group G;

(f) the at least one marker locus comprises S06818-3-Q2 or a markerclosely linked thereto on linkage group G;

(g) the at least one marker locus comprises S06820-1-Q3 or a markerclosely linked thereto on linkage group G;

(h) the at least one marker locus comprises S06821-1-Q2 or a markerclosely linked thereto on linkage group G;

(i) the at least one marker locus comprises S16001-001-Q001 or a markerclosely linked thereto on linkage group G;

(j) the at least one marker locus is between about marker Satt309 andBARC-012285-01798 on linkage group G;

(k) the at least one marker locus is between about markerBARC-015371-01813 and BARCSOYSSR_(—)18_(—)0093 on linkage group G;

(l) the at least one marker locus is between about markerBARC-030055-06792 and BARC-025777-05064 on linkage group G;

(m) the at least one marker locus is between about markerBARC-015371-01813 and BARCSOYSSR_(—)18_(—)0093 on linkage group G;

(n) the at least one marker locus is between about markerBARC-015371-01813 and BARCSOYSSR_(—)18_(—)0093 on linkage group G; or

(o) the at least one marker locus comprises at least one of Gm18:926125;Gm18:1138152; Gm18:1517146; Gm18:1518206; Gm18:1520624; Gm18:1520675;Gm18:1520743; Gm18:1524498; Gm18:1548716; Gm18:1550153; Gm18:1550231;Gm18:1552799; Gm18:1554392; Gm18:1554570; Gm18:1554604; Gm18:1554689;Gm18:1555210; Gm18:1560043; Gm18:1560088; Gm18:1560390; Gm18:1560442;Gm18:1560784; Gm18:1561009; Gm18:1561190; Gm18:1561429; Gm18:1561725;Gm18:1562884; Gm18:1563153; Gm18:1564092; Gm18:1565225; Gm18:1565646;Gm18:1566882; Gm18:1567685; Gm18:1567843; Gm18:1568490; Gm18:1568999;Gm18:1569035; Gm18:1569146; Gm18:1570660; Gm18:1572368; Gm18:1577559;Gm18:1578727; Gm18:1579201; Gm18:1579270; Gm18:1579707; Gm18:1579708;Gm18:1581688; Gm18:1583772; Gm18:1584054; Gm18:1584659; Gm18:1589032;Gm18:1595321; Gm18:1598101; Gm18:1599717; Gm18:1599752; Gm18:1599841;Gm18:1600011; Gm18:1600033; Gm18:1600179; Gm18:1601192; Gm18:1601614;Gm18:1602244; Gm18:1603722; Gm18:1604031; Gm18:1605443; Gm18:1606442;Gm18:1606566; Gm18:1606647; Gm18:1609397; Gm18:1610935; Gm18:1612466;Gm18:1612553; Gm18:1614300; Gm18:1614960 Gm18:1618118; Gm18:1626263;Gm18:1626278; Gm18:1627202; Gm18:1627204; Gm18:1629930; Gm18:1634611;Gm18:1643225; Gm18:1653887; Gm18:1654681; Gm18:1654687; Gm18:1657025;Gm18:1680507; Gm18:1700832; Gm18:1700885; Gm18:1701854; Gm18:1702482;Gm18:1702563; Gm18:1702741; Gm18:1703321; Gm18:1706708; Gm18:1706842;Gm18:1707082; Gm18:1707115; Gm18:1707377; Gm18:1708549; Gm18:1717352;Gm18:1721829; Gm18:1723649; Gm18:1723650; Gm18:1724082; Gm18:172553;Gm18:1725630; Gm18:1725815; Gm18:1725932; Gm18:1725991; Gm18:1726068;Gm18:1727330; Gm18:1727343; Gm18:1727903; Gm18:1728146; Gm18:1728824;Gm18:1729347 Gm18:1729673; Gm18:1729866; Gm18:1730855; Gm18:1731068;Gm18:1731184; Gm18:1731725; Gm18:1731938; Gm18:1734691; Gm18:1735510;Gm18:1740118; Gm18:1747766; Gm18:1751156; Gm18:1752808; Gm18:1754310;Gm18:1754895; Gm18:1759167; Gm18:1759307; Gm18:1761263; Gm18:1762686;Gm18:1763519; Gm18:1768783; Gm18:1768805; Gm18:1769619; Gm18:1773903;Gm18:1773911; Gm18:1778021; Gm18:1783028; Gm18:1783194; Gm18:1783357;Gm18:1785320; Gm18:1787549; Gm18:1789215; Gm18:1789352; Gm18:1789553;Gm18:1789934; Gm18:1805509; Gm18:1859739; Gm18:1863987; Gm18:1864738;Gm18:1877951; Gm18:1881755; Gm18:1607524; Gm18:1888247; Gm18:1845911;Gm18:1846008; Gm18:1565826; or Gm18:1918014; or a marker closely linkedthereto on linkage group G.

20. The isolated polynucleotide of embodiment 19, wherein thepolynucleotide comprises:

(a) a polynucleotide comprising SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45,46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63,64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81,82, 83, 84, 85, 86, 87, 88, 89, 100, 101, 102, 121, 122, 123, 124, 125,126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 140, 141,144, 145, 148, 149, 152, 153, 156, 157, 160, 161, 164, 165, 168, or 169;

(b) a polynucleotide having at least 90% sequence identity to thepolynucleotides set forth in part (a); or

(c) a polynucleotide comprising at least 10 contiguous nucleotides ofthe polynucleotides set forth in part (a).

21. A kit for detecting or selecting at least one soybean plant orsoybean germplasm with improved resistance to soybean cyst nematode, thekit comprising:

a) a primer or a probe for detecting one or more marker loci associatedwith resistance to soybean cyst nematode, wherein the primer or probeare capable of detecting a marker locus, wherein:

-   -   (i) the at least one marker locus comprises S08271-1-Q2 or a        marker closely linked thereto on linkage group G;    -   (ii) the at least one marker locus comprises P7659A-2 or a        marker closely linked thereto on linkage group G;    -   (iii) the at least one marker locus comprises S08051-1-Q1 or a        marker closely linked thereto on linkage group G;    -   (iv) the at least one marker locus comprises S07158-1-Q1 or a        marker closely linked thereto on linkage group G;    -   (v) the at least one marker locus comprises S07159-1-Q1 or a        marker closely linked thereto on linkage group G;    -   (vi) the at least one marker locus comprises S06818-3-Q2 or a        marker closely linked thereto on linkage group G;    -   (vii) the at least one marker locus comprises S06820-1-Q3 or a        marker closely linked thereto on linkage group G;    -   (iix) the at least one marker locus comprises S06821-1-Q2 or a        marker closely linked thereto on linkage group G;    -   (ix) the at least one marker locus comprises S16001-001-Q001 or        a marker closely linked thereto on linkage group G;    -   (x) the at least one marker locus is between about marker        Satt309 and BARC-012285-01798 on linkage group G;    -   (xi) the at least one marker locus is between about marker        BARC-015371-01813 and BARCSOYSSR_(—)18_(—)0093 on linkage group        G;    -   (xii) the at least one marker locus is between about marker        BARC-030055-06792 and BARC-025777-05064 on linkage group G;    -   (xiii) the at least one marker locus is between about marker        BARC-015371-01813 and BARCSOYSSR_(—)18_(—)0093 on linkage group        G;    -   (xiv) the at least one marker locus is between about marker        BARC-015371-01813 and BARCSOYSSR_(—)18_(—)0093 on linkage group        G; or    -   (xv) the at least one marker locus comprises at least one of        Gm18:926125; Gm18:1138152; Gm18:1517146; Gm18:1518206;        Gm18:1520624; Gm18:1520675; Gm18:1520743; Gm18:1524498;        Gm18:1548716; Gm18:1550153; Gm18:1550231; Gm18:1552799;        Gm18:1554392; Gm18:1554570; Gm18:1554604; Gm18:1554689;        Gm18:1555210; Gm18:1560043; Gm18:1560088; Gm18:1560390;        Gm18:1560442; Gm18:1560784; Gm18:1561009; Gm18:1561190;        Gm18:1561429; Gm18:1561725; Gm18:1562884; Gm18:1563153;        Gm18:1564092; Gm18:1565225; Gm18:1565646; Gm18:1566882;        Gm18:1567685; Gm18:1567843; Gm18:1568490; Gm18:1568999;        Gm18:1569035; Gm18:1569146; Gm18:1570660; Gm18:1572368;        Gm18:1577559; Gm18:1578727; Gm18:1579201; Gm18:1579270;        Gm18:1579707; Gm18:1579708; Gm18:1581688; Gm18:1583772;        Gm18:1584054; Gm18:1584659; Gm18:1589032; Gm18:1595321;        Gm18:1598101; Gm18:1599717; Gm18:1599752; Gm18:1599841;        Gm18:1600011; Gm18:1600033; Gm18:1600179; Gm18:1601192;        Gm18:1601614; Gm18:1602244; Gm18:1603722; Gm18:1604031;        Gm18:1605443; Gm18:1606442; Gm18:1606566; Gm18:1606647;        Gm18:1609397; Gm18:1610935; Gm18:1612466; Gm18:1612553;        Gm18:1614300; Gm18:1614960 Gm18:1618118; Gm18:1626263;        Gm18:1626278; Gm18:1627202; Gm18:1627204; Gm18:1629930;        Gm18:1634611; Gm18:1643225; Gm18:1653887; Gm18:1654681;        Gm18:1654687; Gm18:1657025; Gm18:1680507; Gm18:1700832;        Gm18:1700885; Gm18:1701854; Gm18:1702482; Gm18:1702563;        Gm18:1702741; Gm18:1703321; Gm18:1706708; Gm18:1706842;        Gm18:1707082; Gm18:1707115; Gm18:1707377; Gm18:1708549;        Gm18:1717352; Gm18:1721829; Gm18:1723649; Gm18:1723650;        Gm18:1724082; Gm18:172553; Gm18:1725630; Gm18:1725815;        Gm18:1725932; Gm18:1725991; Gm18:1726068; Gm18:1727330;        Gm18:1727343; Gm18:1727903; Gm18:1728146; Gm18:1728824;        Gm18:1729347 Gm18:1729673; Gm18:1729866; Gm18:1730855;        Gm18:1731068; Gm18:1731184; Gm18:1731725; Gm18:1731938;        Gm18:1734691; Gm18:1735510; Gm18:1740118; Gm18:1747766;        Gm18:1751156; Gm18:1752808; Gm18:1754310; Gm18:1754895;        Gm18:1759167; Gm18:1759307; Gm18:1761263; Gm18:1762686;        Gm18:1763519; Gm18:1768783; Gm18:1768805; Gm18:1769619;        Gm18:1773903; Gm18:1773911; Gm18:1778021; Gm18:1783028;        Gm18:1783194; Gm18:1783357; Gm18:1785320; Gm18:1787549;        Gm18:1789215; Gm18:1789352; Gm18:1789553; Gm18:1789934;        Gm18:1805509; Gm18:1859739; Gm18:1863987; Gm18:1864738;        Gm18:1877951; Gm18:1881755; Gm18:1607524; Gm18:1888247;        Gm18:1845911; Gm18:1846008; Gm18:1565826; or Gm18:1918014; or a        marker closely linked thereto on linkage group G; and,

b) instructions for using the primers or probes for detecting the one ormore marker loci and correlating the detected marker loci with predictedresistance to soybean cyst nematode.

EXPERIMENTAL

The following examples are offered to illustrate, but not to limit theclaimed invention. It is understood that the examples and embodimentsdescribed herein are for illustrative purposes only, and persons skilledin the art will recognize various reagents or parameters that can bealtered without departing from the spirit of the invention or the scopeof the appended claims.

Soybean Sequence and SNP Marker Assays Associated with Soybean CystNematode Resistance, Rhg1

SNP markers for the Rhg1 locus (Soybean Cyst Nematode Resistance) onLinkage Group G have been produced, as well as, markers geneticallylinked to these markers. Markers from this region are relevant inbreeding populations and will facilitate selection of soybean plantswith resistance to SCN at the Rhg1 locus tracing back to PI437654,Peking, and/or PI88788, as well as stacks with other marker assistedtraits, including yield genes.

Previously, bioassay procedures for screening soybean plants against areference list Soybean Cyst nematode races were used to determineresistance allele state. These assays are expensive and somewhatvariable. These markers and their association with the trait phenotypein relevant breeding populations have been optimized. The markers, andadditional SNPs linked to these markers, allow for a much more efficientprocess of selecting and breeding. Markers also facilitate stackingsources of resistance and stacks with other important traits insoybeans, including yield. These markers and those linked to thesemarkers, allow for identification and selection of plants in a highlyefficient manner, without the need for bioassay work.

Example 1

Markers were developed to characterize, identify, and/or selectresistant or susceptible alleles at the Rhg1 locus on linkage group G(ch 18). Markers were screened against various known resistant andsusceptible parents.

Marker S08271-1-Q2 was developed to identify alleles associated with SCNphenotype, this marker detects an A/T polymorphism at position 1749394on ch 18, which is likely derived from PI88788. During development, thismarker was validated against SCN resistant line BSR101, and susceptibleline P1437654. The marker was further validated and confirmed against apanel of 31 varieties which included proprietary experimental lines,proprietary commercial lines, and public lines.

TABLE 8 Assay conditions: H20  4.28 ul Hot Tub buffer  0.5 ul Rox Dye(50X) 0.075 ul DNTPs(24 mM each) 0.039 ul Primer(100 uM) 0.0375 ul Primer(100 uM) 0.0375 ul  Primer(100 uM) 0.0375 ul  FAM Probe(100 uM0.005 ul VIC Probe(100 uM 0.005 ul Hot Tub enzyme 0.025 ul Total volume5.005 ul

Further development and testing was done to optimize the marker systemfor high throughput analysis of soybean. From this testing, S08271-1-Q2was chosen for high throughput analysis needs, but other versions can beused to detect the polymorphism. There is a 5 bp deletion in the region,the S08271 forward primer is inside of this indel, and avoids any assaydifficulties that may arise from this deletion.

TABLE 9 Optimization: S08271- S08271- Tcaagtatcgcgcaagctc S08271-Catggtttctcttatcttatracattg S08271- S08271- 1-Q1 F4 (SEQ ID NO: 121) R3(SEQ ID NO: 122 ) and 1-PB3 1-PB4 CAATTCATGGTTTCTCTTATRACATT(SEQ ID NO: 123) S08271- S08271- CattgttgccaagtaatactactatataaattcS08271- Tcaagtatcgcgcaagctc S08271- S08271- 1-Q2 F1 (SEQ ID NO: 124) R1(SEQ ID NO: 125) 1-PB1 1-PB2 S08271- S08271- AttcgcccttcatggtttctS08271- Gcaagctcctgcaaggtatt S08271- S08271- 1-Q3 F2 (SEQ ID NO: 126) R2(SEQ ID NO: 127) 1-PB1 1-PB2 S08271- S08271- CtgagtcttatcattctgtggattgS08271- Gcaagctcctgcaaggtatt S08271- S08271- 1-Q4 F3 (SEQ ID NO: 128) R2(SEQ ID NO: 129) 1-PB1 1-PB2 S08271- S08271-Cattgttgccaagtaatactactatataaattc S08271- Tcaagtatcgcgcaagctc S08271-S08271- 1-Q5 F1 (SEQ ID NO: 130) R1 (SEQ ID NO: 131) 1-PB3 1-PB4 F4 andR1 are the same primer. Note:

TABLE 10 S08271-1- 6FAM- S08271-1- VIC- PB1 TGGGTTTCAGATAAC PB2TGGGTTTCTGATAACC (SEQ ID NO: 132) (SEQ ID NO: 133) S08271-1-6FAM-accacggttatcTgaa S08271-1- VIC-accacggttatcAgaa PB3(SEQ ID NO: 134) PB4 (SEQ ID NO: 135)

Similar development, testing and analysis was done to produce additionalmarkers to detect polymorphisms associated with the Rhg1 locus andsoybean cyst nematode resistance, with the results of this worksummarized in the Tables provided herein. The markers were validatedagainst the panel of SCN resistant or susceptible varieties describedabove. The markers are capable of detecting SCN loci likely derived fromone or more of PI88788, Peking, PI437654, as well markers from othersources. These markers may have further been optimized for robust andconsistent performance in high throughput assay conditions.

These markers can be used in other assays or with other assayconditions, Some markers were assayed under additional conditions. Forexample, S06818-3-Q2, S06820-Q3, and S06821-1-Q2 were tested under thefollowing conditions.

The parameters used for the TaqMan assay are as follows:

TABLE 11 Cycle Settings 94° C. 120 sec  1 cycle 60° C. 60 sec 72° C.  1sec 40 cycles 94° C. 30 sec

TABLE 12 Assay Mix 1x (ul) DNA (1.5 ng) - dried down in assay plate —ddH₂0 3.95 Hottub buffer 0.5 dNTP (2.5 mM) 0.375 Primer 1 + Primer 2(100 uM F + R) 0.02 Probe 1 (10 uM) 0.05 Probe 2 (10 uM) 0.05 Hottubenzyme 0.025 Rox dye (50x) 0.075 Total 5.05

Example 2

Using a case-control association analysis, the Rhg1 locus from Pekingassociated with resistance to soybean cyst nematode (SCN) wasfine-mapped to a region between 1548716-1881755 bp on Gm18 (Lg G). A setof 158 SNPs were identified in this region that perfectly differentiatehighly tolerate from susceptible lines. These markers are ideal formarker-assisted selection of SCN resistance.

Phenotypic data for selected case group lines was based on lab screeningand pedigree information. DNA was prepped using standard Illumina TruSeqchemistry. Selected resistant and susceptible soybean lines formed thecase group and were sequenced to ˜0.5-40× genome coverage on an IlluminaHiSeq2000. SNPs were called using a proprietary software to automate theprocess, missing data was imputed using a separate proprietary software.Haploview was used to conduct a case-control association analysis on aset of 12,449 SNPs identified in the region from 688871-2675880 bp onGm18. The case group comprised 41 public and proprietary soybean linessusceptible to SCN and the control group comprised 7 public andproprietary lines with resistance derived from Peking. FollowingHaploview filtering using the settings noted below, 12,093 SNPs remainedin the analysis.

Haploview Settings:

Do Association Test

Case/Control Data

Ignore Pairwise comparisons of markers >10 kb apart

Exclude individuals with >50% missing genotypes

HW p-value cutoff: 0.0

Min genotype %:50

Max # mendel errors: 1

Minimum minor allele freq.: 0.05

*Physical positions are based on the Glymal Williams82 soybean referenceassembly from JGI.

The case-control analysis identified several SNPs in linkagedisequilibrium with Rhg1 (Peking) phenotypic scores. The case-controlassociation analysis using 12,093 SNPs reveals a peak of allele tophenotype association between 1548716-1881755 bp on Gm18 (Lg G),suggesting that Rhg1 from Peking is in this region, as evaluated using aplot of chi square values. 158 SNPs have a perfect association between41 susceptible (case) and 7 resistant (control) lines (Table 13). Thesemarkers are ideal for TaqMan assay design, or for evaluation by othermethods, including sequencing, hybridization, or other technologies.Numerous additional SNPs analyzed here that are linked to region but arenot in perfect LD with trait could be very informative markers when usedin select germplasm.

TABLE 13 Phys Case, Control Case, Control Chi P SNP Name Pos sus PekingRatio Counts Frequencies square value Marker Gm18: 926125 926125 T A46:0, 0:2 1.000, 0.000 48 4.26E−12 Gm18: 1138152 1138152 G A 54:0, 0:21.000, 0.000 56 7.25E−14 Gm18: 1517146 1517146 G C 72:0, 0:10 1.000,0.000 82 1.36E−19 Gm18: 1518206 1518206 A G 72:0, 0:12 1.000, 0.000 844.95E−20 Gm18: 1520624 1520624 A T 60:0, 0:6 1.000, 0.000 66 4.51E−16Gm18: 1520675 1520675 C T 64:0, 0:8 1.000, 0.000 72 2.15E−17 Gm18:1520743 1520743 G A 68:0, 0:8 1.000, 0.000 76 2.84E−18 Gm18: 15244981524498 G T 64:0, 0:12 1.000, 0.000 76 2.84E−18 Gm18: 1548716 1548716 CT 74:0, 0:12 1.000, 0.000 86 1.80E−20 Gm18: 1550153 1550153 T A 74:0,0:8 1.000, 0.000 82 1.36E−19 Gm18: 1550231 1550231 A T 64:0, 0:8 1.000,0.000 72 2.15E−17 Gm18: 1552799 1552799 C A 78:0, 0:14 1.000, 0.000 928.67E−22 Gm18: 1554392 1554392 T G 68:0, 0:10 1.000, 0.000 78 1.03E−18Gm18: 1554570 1554570 A C 74:0, 0:12 1.000, 0.000 86 1.80E−20 Gm18:1554604 1554604 A G 70:0, 0:14 1.000, 0.000 84 4.95E−20 Gm18: 15546891554689 T C 66:0, 0:10 1.000, 0.000 76 2.84E−18 Gm18: 1555210 1555210 CG 60:0, 0:6 1.000, 0.000 66 4.51E−16 Gm18: 1560043 1560043 T A 68:0,0:10 1.000, 0.000 78 1.03E−18 Gm18: 1560088 1560088 C T 74:0, 0:121.000, 0.000 86 1.80E−20 Gm18: 1560390 1560390 A C 66:0, 0:12 1.000,0.000 78 1.03E−18 Gm18: 1560442 1560442 T A 66:0, 0:12 1.000, 0.000 781.03E−18 Gm18: 1560784 1560784 A G 76:0, 0:14 1.000, 0.000 90 2.38E−21Gm18: 1561009 1561009 G A 78:0, 0:14 1.000, 0.000 92 8.67E−22 Gm18:1561190 1561190 T A 76:0, 0:12 1.000, 0.000 88 6.55E−21 Gm18: 15614291561429 C T 64:0, 0:8 1.000, 0.000 72 2.15E−17 Gm18: 1561725 1561725 A T62:0, 0:10 1.000, 0.000 72 2.15E−17 Gm18: 1562884 1562884 A G 74:0, 0:141.000, 0.000 88 6.55E−21 Gm18: 1563153 1563153 G T 74:0, 0:14 1.000,0.000 88 6.55E−21 Gm18: 1564092 1564092 A T 76:0, 0:14 1.000, 0.000 902.38E−21 Gm18: 1565225 1565225 G A 76:0, 0:14 1.000, 0.000 90 2.38E−21Gm18: 1565646 1565646 T G 78:0, 0:14 1.000, 0.000 92 8.67E−22 Gm18:1566882 1566882 C T 72:0, 0:8 1.000, 0.000 80 3.74E−19 Gm18: 15676851567685 C T 72:0, 0:8 1.000, 0.000 80 3.74E−19 Gm18: 1567843 1567843 T A72:0, 0:10 1.000, 0.000 82 1.36E−19 Gm18: 1568490 1568490 A C 76:0, 0:141.000, 0.000 90 2.38E−21 Gm18: 1568999 1568999 C T 72:0, 0:14 1.000,0.000 86 1.80E−20 Gm18: 1569035 1569035 G T 70:0, 0:12 1.000, 0.000 821.36E−19 Gm18: 1569146 1569146 C T 66:0, 0:12 1.000, 0.000 78 1.03E−18Gm18: 1570660 1570660 T C 78:0, 0:12 1.000, 0.000 90 2.38E−21 Gm18:1572368 1572368 C T 76:0, 0:14 1.000, 0.000 90 2.38E−21 Gm18: 15775591577559 T A 62:0, 0:2 1.000, 0.000 64 1.24E−15 Gm18: 1578727 1578727 G T70:0, 0:14 1.000, 0.000 84 4.95E−20 Gm18: 1579201 1579201 G A 74:0, 0:121.000, 0.000 86 1.80E−20 Gm18: 1579270 1579270 A G 72:0, 0:14 1.000,0.000 86 1.80E−20 Gm18: 1579707 1579707 T G 76:0, 0:14 1.000, 0.000 902.38E−21 Gm18: 1579708 1579708 C T 76:0, 0:14 1.000, 0.000 90 2.38E−21S08051-1 Gm18: 1581688 1581688 T A 74:0, 0:12 1.000, 0.000 86 1.80E−20Gm18: 1583772 1583772 G A 70:0, 0:12 1.000, 0.000 82 1.36E−19 Gm18:1584054 1584054 A G 78:0, 0:12 1.000, 0.000 90 2.38E−21 Gm18: 15846591584659 G C 72:0, 0:14 1.000, 0.000 86 1.80E−20 Gm18: 1589032 1589032 CT 78:0, 0:14 1.000, 0.000 92 8.67E−22 Gm18: 1595321 1595321 T C 74:0,0:14 1.000, 0.000 88 6.55E−21 Gm18: 1598101 1598101 G T 70:0, 0:101.000, 0.000 80 3.74E−19 Gm18: 1599717 1599717 G A 66:0, 0:14 1.000,0.000 80 3.74E−19 Gm18: 1599752 1599752 A G 74:0, 0:12 1.000, 0.000 861.80E−20 Gm18: 1599841 1599841 C T 56:0, 0:2 1.000, 0.000 58 2.62E−14Gm18: 1600011 1600011 C T 56:0, 0:10 1.000, 0.000 66 4.51E−16 Gm18:1600033 1600033 C T 50:0, 0:8 1.000, 0.000 58 2.62E−14 Gm18: 16001791600179 A T 54:0, 0:12 1.000, 0.000 66 4.51E−16 Gm18: 1601192 1601192 TC 74:0, 0:12 1.000, 0.000 86 1.80E−20 Gm18: 1601614 1601614 A G 76:0,0:14 1.000, 0.000 90 2.38E−21 Gm18: 1602244 1602244 C G 74:0, 0:121.000, 0.000 86 1.80E−20 Gm18: 1603722 1603722 C T 64:0, 0:12 1.000,0.000 76 2.84E−18 Gm18: 1604031 1604031 A G 76:0, 0:12 1.000, 0.000 886.55E−21 Gm18: 1605443 1605443 A T 60:0, 0:10 1.000, 0.000 70 5.93E−17Gm18: 1606442 1606442 T A 66:0, 0:14 1.000, 0.000 80 3.74E−19 Gm18:1606566 1606566 A T 56:0, 0:14 1.000, 0.000 70 5.93E−17 Gm18: 16066471606647 C T 56:0, 0:8 1.000, 0.000 64 1.24E−15 Gm18: 1609397 1609397 C A76:0, 0:10 1.000, 0.000 86 1.80E−20 Gm18: 1610935 1610935 A G 58:0, 0:101.000, 0.000 68 1.64E−16 Gm18: 1612466 1612466 G A 68:0, 0:8 1.000,0.000 76 2.84E−18 Gm18: 1612553 1612553 G A 70:0, 0:4 1.000, 0.000 747.81E−18 Gm18: 1614300 1614300 T A 68:0, 0:10 1.000, 0.000 78 1.03E−18Gm18: 1614960 1614960 A T 76:0, 0:14 1.000, 0.000 90 2.38E−21 Gm18:1618118 1618118 T A 78:0, 0:14 1.000, 0.000 92 8.67E−22 Gm18: 16262631626263 T G 52:0, 0:4 1.000, 0.000 56 7.25E−14 Gm18: 1626278 1626278 G A54:0, 0:8 1.000, 0.000 62 3.43E−15 Gm18: 1627202 1627202 A T 50:0, 0:21.000, 0.000 52 5.55E−13 Gm18: 1627204 1627204 C A 48:0, 0:2 1.000,0.000 50 1.54E−12 Gm18: 1629930 1629930 T C 54:0, 0:12 1.000, 0.000 664.51E−16 Gm18: 1634611 1634611 A T 64:0, 0:2 1.000, 0.000 66 4.51E−16Gm18: 1643225 1643225 C G 70:0, 0:12 1.000, 0.000 82 1.36E−19 Gm18:1653887 1653887 C T 74:0, 0:12 1.000, 0.000 86 1.80E−20 Gm18: 16546811654681 T A 70:0, 0:12 1.000, 0.000 82 1.36E−19 Gm18: 1654687 1654687 GC 70:0, 0:10 1.000, 0.000 80 3.74E−19 Gm18: 1657025 1657025 A T 66:0,0:14 1.000, 0.000 80 3.74E−19 Gm18: 1680507 1680507 T C 74:0, 0:8 1.000,0.000 82 1.36E−19 Gm18: 1700832 1700832 C T 62:0, 0:14 1.000, 0.000 762.84E−18 Gm18: 1700885 1700885 G A 58:0, 0:8 1.000, 0.000 66 4.51E−16Gm18: 1701854 1701854 A G 64:0, 0:14 1.000, 0.000 78 1.03E−18 Gm18:1702482 1702482 C T 62:0, 0:10 1.000, 0.000 72 2.15E−17 Gm18: 17025631702563 C A 46:0, 0:12 1.000, 0.000 58 2.62E−14 Gm18: 1702741 1702741 TC 68:0, 0:10 1.000, 0.000 78 1.03E−18 Gm18: 1703321 1703321 T A 78:0,0:14 1.000, 0.000 92 8.67E−22 Gm18: 1706708 1706708 G A 76:0, 0:121.000, 0.000 88 6.55E−21 Gm18: 1706842 1706842 C G 74:0, 0:12 1.000,0.000 86 1.80E−20 Gm18: 1707082 1707082 G A 76:0, 0:14 1.000, 0.000 902.38E−21 Gm18: 1707115 1707115 A G 76:0, 0:14 1.000, 0.000 90 2.38E−21Gm18: 1707377 1707377 T C 68:0, 0:10 1.000, 0.000 78 1.03E−18 Gm18:1708549 1708549 G A 64:0, 0:12 1.000, 0.000 76 2.84E−18 Gm18: 17173521717352 G T 64:0, 0:12 1.000, 0.000 76 2.84E−18 Gm18: 1721829 1721829 AT 76:0, 0:14 1.000, 0.000 90 2.38E−21 Gm18: 1723649 1723649 C A 78:0,0:14 1.000, 0.000 92 8.67E−22 Gm18: 1723650 1723650 A T 78:0, 0:141.000, 0.000 92 8.67E−22 Gm18: 1724082 1724082 A G 76:0, 0:14 1.000,0.000 90 2.38E−21 Gm18: 1725538 1725538 T G 60:0, 0:6 1.000, 0.000 664.51E−16 Gm18: 1725630 1725630 G C 76:0, 0:12 1.000, 0.000 88 6.55E−21Gm18: 1725815 1725815 G A 74:0, 0:14 1.000, 0.000 88 6.55E−21 Gm18:1725932 1725932 C T 76:0, 0:14 1.000, 0.000 90 2.38E−21 Gm18: 17259911725991 A G 74:0, 0:12 1.000, 0.000 86 1.80E−20 Gm18: 1726068 1726068 GT 78:0, 0:12 1.000, 0.000 90 2.38E−21 Gm18: 1727330 1727330 T C 72:0,0:12 1.000, 0.000 84 4.95E−20 Gm18: 1727343 1727343 A C 72:0, 0:121.000, 0.000 84 4.95E−20 Gm18: 1727903 1727903 C T 78:0, 0:14 1.000,0.000 92 8.67E−22 Gm18: 1728146 1728146 C A 76:0, 0:14 1.000, 0.000 902.38E−21 Gm18: 1728824 1728824 G A 76:0, 0:12 1.000, 0.000 88 6.55E−21Gm18: 1729347 1729347 T C 76:0, 0:12 1.000, 0.000 88 6.55E−21 Gm18:1729673 1729673 A G 76:0, 0:14 1.000, 0.000 90 2.38E−21 Gm18: 17298661729866 C T 76:0, 0:14 1.000, 0.000 90 2.38E−21 Gm18: 1730855 1730855 AT 76:0, 0:14 1.000, 0.000 90 2.38E−21 Gm18: 1731068 1731068 G A 76:0,0:14 1.000, 0.000 90 2.38E−21 Gm18: 1731184 1731184 T A 76:0, 0:121.000, 0.000 88 6.55E−21 Gm18: 1731725 1731725 T C 74:0, 0:14 1.000,0.000 88 6.55E−21 Gm18: 1731938 1731938 G A 74:0, 0:14 1.000, 0.000 886.55E−21 Gm18: 1734691 1734691 C T 76:0, 0:14 1.000, 0.000 90 2.38E−21Gm18: 1735510 1735510 T A 78:0, 0:12 1.000, 0.000 90 2.38E−21 Gm18:1740118 1740118 C T 76:0, 0:14 1.000, 0.000 90 2.38E−21 Gm18: 17477661747766 A T 74:0, 0:12 1.000, 0.000 86 1.80E−20 Gm18: 1751156 1751156 CT 70:0, 0:12 1.000, 0.000 82 1.36E−19 Gm18: 1752808 1752808 A T 54:0,0:10 1.000, 0.000 64 1.24E−15 Gm18: 1754310 1754310 A G 74:0, 0:141.000, 0.000 88 6.55E−21 Gm18: 1754895 1754895 T A 50:0, 0:12 1.000,0.000 62 3.43E−15 Gm18: 1759167 1759167 G A 72:0, 0:12 1.000, 0.000 844.95E−20 Gm18: 1759307 1759307 G A 76:0, 0:14 1.000, 0.000 90 2.38E−21Gm18: 1761263 1761263 A C 62:0, 0:14 1.000, 0.000 76 2.84E−18 Gm18:1762686 1762686 A G 74:0, 0:14 1.000, 0.000 88 6.55E−21 Gm18: 17635191763519 T A 76:0, 0:12 1.000, 0.000 88 6.55E−21 Gm18: 1768783 1768783 CA 74:0, 0:14 1.000, 0.000 88 6.55E−21 Gm18: 1768805 1768805 A G 74:0,0:14 1.000, 0.000 88 6.55E−21 Gm18: 1769619 1769619 T A 76:0, 0:141.000, 0.000 90 2.38E−21 Gm18: 1773903 1773903 T C 72:0, 0:6 1.000,0.000 78 1.03E−18 Gm18: 1773911 1773911 A T 74:0, 0:6 1.000, 0.000 803.74E−19 Gm18: 1778021 1778021 A G 72:0, 0:12 1.000, 0.000 84 4.95E−20Gm18: 1783028 1783028 G A 70:0, 0:10 1.000, 0.000 80 3.74E−19 Gm18:1783194 1783194 C T 62:0, 0:12 1.000, 0.000 74 7.81E−18 Gm18: 17833571783357 G T 70:0, 0:14 1.000, 0.000 84 4.95E−20 Gm18: 1785320 1785320 TG 78:0, 0:10 1.000, 0.000 88 6.55E−21 Gm18: 1787549 1787549 A G 76:0,0:14 1.000, 0.000 90 2.38E−21 Gm18: 1789215 1789215 G A 78:0, 0:141.000, 0.000 92 8.67E−22 Gm18: 1789352 1789352 G C 76:0, 0:14 1.000,0.000 90 2.38E−21 Gm18: 1789553 1789553 C T 78:0, 0:12 1.000, 0.000 902.38E−21 Gm18: 1789934 1789934 T A 78:0, 0:12 1.000, 0.000 90 2.38E−21Gm18: 1805509 1805509 T C 54:0, 0:4 1.000, 0.000 58 2.62E−14 Gm18:1859739 1859739 C G 68:0, 0:12 1.000, 0.000 80 3.74E−19 Gm18: 18639871863987 C T 76:0, 0:14 1.000, 0.000 90 2.38E−21 Gm18: 1864738 1864738 AG 78:0, 0:14 1.000, 0.000 92 8.67E−22 Gm18: 1877951 1877951 T C 74:0,0:14 1.000, 0.000 88 6.55E−21 Gm18: 1881755 1881755 G A 76:0, 0:141.000, 0.000 90 2.38E−21

Additionally, the markers on LG G summarized in Table 14 were alsoincluded in this study.

TABLE 14 Case, Control Phys Ratio Case, Control Chi Marker Genetic PosSUS Peking Counts Frequencies square P value Source S08271-1-Q2 10.21749394 A T 42:28, 0:14 0.600, 0.000 16.8 4.15E−05 Pi88788 (P10355B-1)P7659A-2 12.3 1580305 C T Pi88788 S08051-1-Q1 9.3 1579707 T G  76:0,0:14 1.000, 0.000 90 2.38E−21 Peking, (P7659A-1) 1579708 C T  76:0, 0:141.000, 0.000 90 2.38E−21 PI437654 S07158-1-Q1 12.3 2098742 G T 24:54,2:12 0.308, 0.143 1.591 0.2072 PI437654, (P5219A-1) 2098741 T G 24:54,2:12 0.308, 0.143 1.591 0.2072 Pi88788, Peking S07159-1-Q1 12.3 2095977A A  2:76, 0:14 0.026, 0.000 0.367 0.5447 PI437654 (P5219A-2)S06818-3-Q2 9.2 1573060 C G 66:10, 0:12 0.868, 0.000 41.684 1.07E−10Peking or Pi88788 S06820-1-Q3 9.2 1571774 A G 66:10, 0:14 0.868, 0.00045.592 1.46E−11 Peking or Pi88788 S06821-1-Q2 9.2 1563924 G T 64:10,0:14 0.865, 0.000 44.396 2.68E−11 Peking or Pi88788 S16001-001- 9.41607524 A A Pi88788 Q001

Example 3

Using a case-control association analysis, the Rhg1 locus from P188788associated with resistance to soybean cyst nematode (SCN) wasfine-mapped to a region between 1477584-1933546 bp on Gm18 (Lg G). A setof 6 SNPs were identified in this region that perfectly differentiatehighly PI88788 derived lines from susceptible lines. These markers areideal for marker-assisted selection of SCN resistance.

Phenotypic data for selected case group lines was based on lab screeningand pedigree information. DNA was prepped using standard Illumina TruSeqchemistry. Selected resistant and susceptible soybean lines formed thecase group and were sequenced to ˜0.5-40× genome coverage on an IlluminaHiSeq2000. SNPs were called using a proprietary software to automate theprocess, missing data was imputed using a separate proprietary software.Haploview was used to conduct a case-control association analysis on aset of 13,147 SNPs identified in the region from 688871-2675880 bp onGm18. The case group comprised 41 public and proprietary soybean linessusceptible to SCN and the control group comprised 78 proprietary lineswith resistance derived from P188788. Following Haploview filteringusing the settings noted below, 10,872 SNPs remained in the analysis.

Haploview Settings:

Do Association Test

Case/Control Data

Ignore Pairwise comparisons of markers >10 kb apart

Exclude individuals with >50% missing genotypes

HW p-value cutoff: 0.0

Min genotype %:50

Max # mendel errors: 1

Minimum minor allele freq.: 0.05

*Physical positions are based on the Glymal Williams82 soybean referenceassembly from JGI.

The case-control analysis identified several SNPs in linkagedisequilibrium with Rhg1 (Peking) phenotypic scores. The case-controlassociation analysis using 10,872 SNPs reveals a peak of allele tophenotype association between 1477584-1933546 bp on Gm18 (Lg G),suggesting that Rhg1 from P188788 is in this region, as evaluated usinga plot of chi square values. 158 SNPs have a perfect association between41 susceptible (case) and 78 resistant (control) lines (Table A). Thesemarkers are ideal for TaqMan assay design, or for evaluation by othermethods, including sequencing, hybridization, or other technologies.Numerous additional SNPs analyzed here that are linked to region but arenot in perfect LD with trait could be very informative markers when usedin select germplasm.

TABLE 15 Case, Control Case, Control Chi Marker Name Phys Pos SUSPi88788 Ratio Counts Frequencies square P value Assay Gm18: 16075241607524 A C 76:0, 0:124 1.000, 0.000 200 2.09E−45 S16001- 001-Q001 Gm18:1888247 1845911 A T 68:0, 0:108 1.000, 0.000 176 3.62E−40 Gm18: 18459111845911 T C 56:0, 0:108 1.000, 0.000 164 1.51E−37 Gm18: 1846008 1846008A G 54:0, 0:100 1.000, 0.000 154 2.32E−35 Gm18: 1565826 1565826 T G74:0, 0:64 1.000, 0.000 138 7.29E−32 Gm18: 1918014 1918014 G A 58:0,0:80 1.000, 0.000 138 7.29E−32Additionally, the markers on LG G summarized in Table B were alsoincluded in this study.

TABLE 16 Case, Control Production Phys Ratio Case, Control Chi P MarkerLg Genetic Pos SUS Pi88788 Counts Frequencies square value SourceS08271-1- G 10.2 1749394 A or T A 28:42, 0:106 0.400, 0.000 50.4221.24E−12 PI88788 Q2 (P10355B- 1) P7659A-2 G 12.3 1580305 C or T T 64:10,4:134 0.865, 0.029 154.477 1.82E−35 PI88788 S08051-1- G 9.3 1579707Peking, Q1 and PI437654 (P7659A-1) 1579708 S07158-1- G 12.3 2098742 T orG G 54:24, 0.692, 0.086 87.315 9.26E−21 PI437654, Q1 12:128 PI88788,(P5219A-1) 2098741 G or T T 54:24, 0.692, 0.086 87.315 9.26E−21 Peking12:128 S07159-1- G 12.3 2095977 PI437654 Q1 (P5219A-2) S06818-3- G 9.21573060 C or G G 66:10, 0:128 0.868, 0.000 164.32 1.29E−37 Peking or Q2PI88788 S06820-1- G 9.2 1571774 A or G 66:10, 2:114 0.868, 0.017 145.441.72E−33 Peking or Q3 PI88788 S06821-1- G 9.2 1563924 G or T T 64:10,2:142 0.865, 0.014 167.686 2.37E−38 Peking or Q2 PI88788 S16001- G 9.41607524 A C 76:0, 0:124 1.000, 0.000 200 2.09E−45 PI88788 001-Q001

All publications and patent applications mentioned in the specificationare indicative of the level of those skilled in the art to which thisinvention pertains. All publications and patent applications are hereinincorporated by reference to the same extent as if each individualpublication or patent application was specifically and individuallyindicated to be incorporated by reference.

Although the foregoing invention has been described in some detail byway of illustration and example for purposes of clarity ofunderstanding, it will be obvious that certain changes and modificationsmay be practiced within the scope of the appended claims.

That which is claimed:
 1. A method of identifying a first soybean plantor a first soybean germplasm that displays improved resistance tosoybean cyst nematode, the method comprising detecting in the genome ofsaid first soybean plant or in the genome of said first soybeangermplasm at least one marker locus that is associated with theresistance, wherein: (a) the at least one marker locus comprisesS08271-1-Q2 or a marker closely linked thereto on linkage group G; (b)the at least one marker locus comprises P7659A-2 or a marker closelylinked thereto on linkage group G; (c) the at least one marker locuscomprises S08051-1-Q1 or a marker closely linked thereto on linkagegroup G; (d) the at least one marker locus comprises S07158-1-Q1 or amarker closely linked thereto on linkage group G; (e) the at least onemarker locus comprises S07159-1-Q1 or a marker closely linked thereto onlinkage group G; (f) the at least one marker locus comprises S06818-3-Q2or a marker closely linked thereto on linkage group G; (g) the at leastone marker locus comprises S06820-1-Q3 or a marker closely linkedthereto on linkage group G; (h) the at least one marker locus comprisesS06821-1-Q2 or a marker closely linked thereto on linkage group G; (i)the at least one marker locus comprises S16001-001-Q001 or a markerclosely linked thereto on linkage group G; (j) the at least one markerlocus is between about marker Satt309 and BARC-012285-01798 on linkagegroup G; (k) the at least one marker locus is between about markerBARC-015371-01813 and BARCSOYSSR_(—)18_(—)0093 on linkage group G; (l)the at least one marker locus is between about marker BARC-030055-06792and BARC-025777-05064 on linkage group G; (m) the at least one markerlocus is between about marker BARC-015371-01813 andBARCSOYSSR_(—)18_(—)0093 on linkage group G; (n) the at least one markerlocus is between about marker BARC-015371-01813 andBARCSOYSSR_(—)18_(—)0093 on linkage group G; or (o) the at least onemarker locus comprises at least one of Gm18:926125; Gm18:1138152;Gm18:1517146; Gm18:1518206; Gm18:1520624; Gm18:1520675; Gm18:1520743;Gm18:1524498; Gm18:1548716; Gm18:1550153; Gm18:1550231; Gm18:1552799;Gm18:1554392; Gm18:1554570; Gm18:1554604; Gm18:1554689; Gm18:1555210;Gm18:1560043; Gm18:1560088; Gm18:1560390; Gm18:1560442; Gm18:1560784;Gm18:1561009; Gm18:1561190; Gm18:1561429; Gm18:1561725; Gm18:1562884;Gm18:1563153; Gm18:1564092; Gm18:1565225; Gm18:1565646; Gm18:1566882;Gm18:1567685; Gm18:1567843; Gm18:1568490; Gm18:1568999; Gm18:1569035;Gm18:1569146; Gm18:1570660; Gm18:1572368; Gm18:1577559; Gm18:1578727;Gm18:1579201; Gm18:1579270; Gm18:1579707; Gm18:1579708; Gm18:1581688;Gm18:1583772; Gm18:1584054; Gm18:1584659; Gm18:1589032; Gm18:1595321;Gm18:1598101; Gm18:1599717; Gm18:1599752; Gm18:1599841; Gm18:1600011;Gm18:1600033; Gm18:1600179; Gm18:1601192; Gm18:1601614; Gm18:1602244;Gm18:1603722; Gm18:1604031; Gm18:1605443; Gm18:1606442; Gm18:1606566;Gm18:1606647; Gm18:1609397; Gm18:1610935; Gm18:1612466; Gm18:1612553;Gm18:1614300; Gm18:1614960 Gm18:1618118; Gm18:1626263; Gm18:1626278;Gm18:1627202; Gm18:1627204; Gm18:1629930; Gm18:1634611; Gm18:1643225;Gm18:1653887; Gm18:1654681; Gm18:1654687; Gm18:1657025; Gm18:1680507;Gm18:1700832; Gm18:1700885; Gm18:1701854; Gm18:1702482; Gm18:1702563;Gm18:1702741; Gm18:1703321; Gm18:1706708; Gm18:1706842; Gm18:1707082;Gm18:1707115; Gm18:1707377; Gm18:1708549; Gm18:1717352; Gm18:1721829;Gm18:1723649; Gm18:1723650; Gm18:1724082; Gm18:172553; Gm18:1725630;Gm18:1725815; Gm18:1725932; Gm18:1725991; Gm18:1726068; Gm18:1727330;Gm18:1727343; Gm18:1727903; Gm18:1728146; Gm18:1728824; Gm18:1729347Gm18:1729673; Gm18:1729866; Gm18:1730855; Gm18:1731068; Gm18:1731184;Gm18:1731725; Gm18:1731938; Gm18:1734691; Gm18:1735510; Gm18:1740118;Gm18:1747766; Gm18:1751156; Gm18:1752808; Gm18:1754310; Gm18:1754895;Gm18:1759167; Gm18:1759307; Gm18:1761263; Gm18:1762686; Gm18:1763519;Gm18:1768783; Gm18:1768805; Gm18:1769619; Gm18:1773903; Gm18:1773911;Gm18:1778021; Gm18:1783028; Gm18:1783194; Gm18:1783357; Gm18:1785320;Gm18:1787549; Gm18:1789215; Gm18:1789352; Gm18:1789553; Gm18:1789934;Gm18:1805509; Gm18:1859739; Gm18:1863987; Gm18:1864738; Gm18:1877951;Gm18:1881755; Gm18:1607524; Gm18:1888247; Gm18:1845911; Gm18:1846008;Gm18:1565826; or Gm18:1918014; or a marker closely linked thereto onlinkage group G.
 2. The method of claim 1, wherein at least two markerloci are detected.
 3. The method of claim 1, wherein the at least twomarker loci comprise a haplotype that is associated with saidresistance.
 4. The method of claim 1, wherein the at least two markerloci comprise a marker profile that is associated with said resistance.5. The method of claim 1, wherein the germplasm is a soybean variety. 6.The method of claim 1, wherein the method further comprises selectingthe first soybean plant or first soybean germplasm or a progeny thereofhaving the at least one marker locus.
 7. The method of claim 6, furthercomprising crossing the selected first soybean plant or first soybeangermplasm with a second soybean plant or second soybean germplasm. 8.The method of claim 7, wherein the second soybean plant or secondsoybean germplasm comprises an exotic soybean strain or an elite soybeanstrain.
 9. The method of claim 1, wherein the detecting comprisesamplifying at least one of said marker loci and detecting the resultingamplified marker amplicon.
 10. The method of claim 9, wherein theamplifying comprises: a) admixing an amplification primer oramplification primer pair for each marker locus being amplified with anucleic acid isolated from the first soybean plant or the first soybeangermplasm, wherein the primer or primer pair is complementary orpartially complementary to a variant or fragment of the genomic locuscomprising the marker locus, and is capable of initiating DNApolymerization by a DNA polymerase using the soybean nucleic acid as atemplate; and b) extending the primer or primer pair in a DNApolymerization reaction comprising a DNA polymerase and a templatenucleic acid to generate at least one amplicon.
 11. The method of claim10, wherein said method comprises amplifying a variant or fragment ofone or more polynucleotides comprising SEQ ID NOs: 103, 104, 105, 106,107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120,138, 139, 142, 143, 146, 147, 150, 151, 154, 155, 158, 159, 162, 163,166, 167, 170 or
 171. 12. The method of claim 10, wherein said primer orprimer pair comprises a variant or fragment of one or morepolynucleotides comprising SEQ ID NOs: 103, 104, 105, 106, 107, 108,109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 138, 139,142, 143, 146, 147, 150, 151, 154, 155, 158, 159, 162, 163, 166, 167,170 or
 171. 13. The method of claim 10, wherein said primer or primerpair comprises a nucleic acid sequence comprising SEQ ID NOs: 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40,41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58,59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76,77, 78, 79, 80, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131,136, 137, 140, 141, 144, 145, 148, 149, 152, 153, 156, 157, 160, 161,164, 165, 168, or 169 or variants or fragments thereof.
 14. The methodof claim 10, wherein said primer pair comprises: a) SEQ ID NOS: 81 and82; b) SEQ ID NOS: 87 and 88; c) SEQ ID NOS: 89 and 90; d) SEQ ID NOS:91 and 92; e) SEQ ID NOS: 93 and 94; f) SEQ ID NOS:95 and 96; g) SEQ IDNOS: 97 and 98; h) SEQ ID NOS: 99 and 100; i) SEQ ID NOS: 101 and 102;j) SEQ ID NOS: 121 and 122; k) SEQ ID NOS: 121 and 123; l) SEQ ID NOS:124 and 125; m) SEQ ID NOS: 126 and 127; n) SEQ ID NOS: 128 and 129; o)SEQ ID NOS: 130 and 131; p) SEQ ID NOS: 136 and 137; q) SEQ ID NOS: 140and 141; r) SEQ ID NOS: 144 and 145; s) SEQ ID NOS: 148 and 149; t) SEQID NOS: 152 and 153; u) SEQ ID NOS: 156 and 157; v) SEQ ID NOS: 160 and161; w) SEQ ID NOS: 164 and 165; or, x) SEQ ID NOS: 168 and
 169. 15. Themethod of claim 10, wherein the method further comprises providing oneor more labeled nucleic acid probes suitable for detection of eachmarker locus being amplified.
 16. The method of claim 15, wherein saidlabeled nucleic acid probe comprises a nucleic acid sequence comprisinga variant or fragment of one or more polynucleotides comprising SEQ IDNOs: 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115,116, 117, 118, 119, 120, 138, 139, 142, 143, 146, 147, 150, 151, 154,155, 158, 159, 162, 163, 166, 167, 170 or 171 or complements thereof.17. The method of claim 15, wherein the labeled nucleic acid probecomprises a nucleic acid sequence comprising SEQ ID NOs: 81, 82, 83, 84,85, 86, 87, 88, 89, 100, 101, 102, 132, 133, 134, or
 135. 18. The methodof claim 1, wherein the detecting comprises DNA sequencing of at leastone of said marker loci.
 19. An isolated polynucleotide capable ofdetecting a marker locus of the soybean genome comprising (a) the atleast one marker locus comprises S08271-1-Q2 or a marker closely linkedthereto on linkage group G; (b) the at least one marker locus comprisesP7659A-2 or a marker closely linked thereto on linkage group G; (c) theat least one marker locus comprises S08051-1-Q1 or a marker closelylinked thereto on linkage group G; (d) the at least one marker locuscomprises S07158-1-Q1 or a marker closely linked thereto on linkagegroup G; (e) the at least one marker locus comprises S07159-1-Q1 or amarker closely linked thereto on linkage group G; (f) the at least onemarker locus comprises S06818-3-Q2 or a marker closely linked thereto onlinkage group G; (g) the at least one marker locus comprises S06820-1-Q3or a marker closely linked thereto on linkage group G; (h) the at leastone marker locus comprises S06821-1-Q2 or a marker closely linkedthereto on linkage group G; (i) the at least one marker locus comprisesS16001-001-Q001 or a marker closely linked thereto on linkage group G;(j) the at least one marker locus is between about marker Satt309 andBARC-012285-01798 on linkage group G; (k) the at least one marker locusis between about marker BARC-015371-01813 and BARCSOYSSR_(—)18_(—)0093on linkage group G; (l) the at least one marker locus is between aboutmarker BARC-030055-06792 and BARC-025777-05064 on linkage group G; (m)the at least one marker locus is between about marker BARC-015371-01813and BARCSOYSSR_(—)18_(—)0093 on linkage group G; (n) the at least onemarker locus is between about marker BARC-015371-01813 andBARCSOYSSR_(—)18_(—)0093 on linkage group G; or (o) the at least onemarker locus comprises at least one of Gm18:926125; Gm18:1138152;Gm18:1517146; Gm18:1518206; Gm18:1520624; Gm18:1520675; Gm18:1520743;Gm18:1524498; Gm18:1548716; Gm18:1550153; Gm18:1550231; Gm18:1552799;Gm18:1554392; Gm18:1554570; Gm18:1554604; Gm18:1554689; Gm18:1555210;Gm18:1560043; Gm18:1560088; Gm18:1560390; Gm18:1560442; Gm18:1560784;Gm18:1561009; Gm18:1561190; Gm18:1561429; Gm18:1561725; Gm18:1562884;Gm18:1563153; Gm18:1564092; Gm18:1565225; Gm18:1565646; Gm18:1566882;Gm18:1567685; Gm18:1567843; Gm18:1568490; Gm18:1568999; Gm18:1569035;Gm18:1569146; Gm18:1570660; Gm18:1572368; Gm18:1577559; Gm18:1578727;Gm18:1579201; Gm18:1579270; Gm18:1579707; Gm18:1579708; Gm18:1581688;Gm18:1583772; Gm18:1584054; Gm18:1584659; Gm18:1589032; Gm18:1595321;Gm18:1598101; Gm18:1599717; Gm18:1599752; Gm18:1599841; Gm18:1600011;Gm18:1600033; Gm18:1600179; Gm18:1601192; Gm18:1601614; Gm18:1602244;Gm18:1603722; Gm18:1604031; Gm18:1605443; Gm18:1606442; Gm18:1606566;Gm18:1606647; Gm18:1609397; Gm18:1610935; Gm18:1612466; Gm18:1612553;Gm18:1614300; Gm18:1614960 Gm18:1618118; Gm18:1626263; Gm18:1626278;Gm18:1627202; Gm18:1627204; Gm18:1629930; Gm18:1634611; Gm18:1643225;Gm18:1653887; Gm18:1654681; Gm18:1654687; Gm18:1657025; Gm18:1680507;Gm18:1700832; Gm18:1700885; Gm18:1701854; Gm18:1702482; Gm18:1702563;Gm18:1702741; Gm18:1703321; Gm18:1706708; Gm18:1706842; Gm18:1707082;Gm18:1707115; Gm18:1707377; Gm18:1708549; Gm18:1717352; Gm18:1721829;Gm18:1723649; Gm18:1723650; Gm18:1724082; Gm18:172553; Gm18:1725630;Gm18:1725815; Gm18:1725932; Gm18:1725991; Gm18:1726068; Gm18:1727330;Gm18:1727343; Gm18:1727903; Gm18:1728146; Gm18:1728824; Gm18:1729347Gm18:1729673; Gm18:1729866; Gm18:1730855; Gm18:1731068; Gm18:1731184;Gm18:1731725; Gm18:1731938; Gm18:1734691; Gm18:1735510; Gm18:1740118;Gm18:1747766; Gm18:1751156; Gm18:1752808; Gm18:1754310; Gm18:1754895;Gm18:1759167; Gm18:1759307; Gm18:1761263; Gm18:1762686; Gm18:1763519;Gm18:1768783; Gm18:1768805; Gm18:1769619; Gm18:1773903; Gm18:1773911;Gm18:1778021; Gm18:1783028; Gm18:1783194; Gm18:1783357; Gm18:1785320;Gm18:1787549; Gm18:1789215; Gm18:1789352; Gm18:1789553; Gm18:1789934;Gm18:1805509; Gm18:1859739; Gm18:1863987; Gm18:1864738; Gm18:1877951;Gm18:1881755; Gm18:1607524; Gm18:1888247; Gm18:1845911; Gm18:1846008;Gm18:1565826; or Gm18:1918014; or a marker closely linked thereto onlinkage group G.
 20. The isolated polynucleotide of claim 19, whereinthe polynucleotide comprises: (a) a polynucleotide comprising SEQ IDNOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37,38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55,56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73,74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 100,101, 102, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132,133, 134, 135, 136, 137, 140, 141, 144, 145, 148, 149, 152, 153, 156,157, 160, 161, 164, 165, 168, or 169; (b) a polynucleotide having atleast 90% sequence identity to the polynucleotides set forth in part(a); or (c) a polynucleotide comprising at least 10 contiguousnucleotides of the polynucleotides set forth in part (a).
 21. A kit fordetecting or selecting at least one soybean plant or soybean germplasmwith improved resistance to soybean cyst nematode, the kit comprising:a) a primer or a probe for detecting one or more marker loci associatedwith resistance to soybean cyst nematode, wherein the primer or probeare capable of detecting a marker locus, wherein: (i) the at least onemarker locus comprises S08271-1-Q2 or a marker closely linked thereto onlinkage group G; (ii) the at least one marker locus comprises P7659A-2or a marker closely linked thereto on linkage group G; (iii) the atleast one marker locus comprises S08051-1-Q1 or a marker closely linkedthereto on linkage group G; (iv) the at least one marker locus comprisesS07158-1-Q1 or a marker closely linked thereto on linkage group G; (v)the at least one marker locus comprises S07159-1-Q1 or a marker closelylinked thereto on linkage group G; (vi) the at least one marker locuscomprises S06818-3-Q2 or a marker closely linked thereto on linkagegroup G; (vii) the at least one marker locus comprises S06820-1-Q3 or amarker closely linked thereto on linkage group G; (iix) the at least onemarker locus comprises S06821-1-Q2 or a marker closely linked thereto onlinkage group G; (ix) the at least one marker locus comprisesS16001-001-Q001 or a marker closely linked thereto on linkage group G;(x) the at least one marker locus is between about marker Satt309 andBARC-012285-01798 on linkage group G; (xi) the at least one marker locusis between about marker BARC-015371-01813 and BARCSOYSSR_(—)18_(—)0093on linkage group G; (xii) the at least one marker locus is between aboutmarker BARC-030055-06792 and BARC-025777-05064 on linkage group G;(xiii) the at least one marker locus is between about markerBARC-015371-01813 and BARCSOYSSR_(—)18_(—)0093 on linkage group G; (xiv)the at least one marker locus is between about marker BARC-015371-01813and BARCSOYSSR_(—)18_(—)0093 on linkage group G; or (xv) the at leastone marker locus comprises at least one of Gm18:926125; Gm18:1138152;Gm18:1517146; Gm18:1518206; Gm18:1520624; Gm18:1520675; Gm18:1520743;Gm18:1524498; Gm18:1548716; Gm18:1550153; Gm18:1550231; Gm18:1552799;Gm18:1554392; Gm18:1554570; Gm18:1554604; Gm18:1554689; Gm18:1555210;Gm18:1560043; Gm18:1560088; Gm18:1560390; Gm18:1560442; Gm18:1560784;Gm18:1561009; Gm18:1561190; Gm18:1561429; Gm18:1561725; Gm18:1562884;Gm18:1563153; Gm18:1564092; Gm18:1565225; Gm18:1565646; Gm18:1566882;Gm18:1567685; Gm18:1567843; Gm18:1568490; Gm18:1568999; Gm18:1569035;Gm18:1569146; Gm18:1570660; Gm18:1572368; Gm18:1577559; Gm18:1578727;Gm18:1579201; Gm18:1579270; Gm18:1579707; Gm18:1579708; Gm18:1581688;Gm18:1583772; Gm18:1584054; Gm18:1584659; Gm18:1589032; Gm18:1595321;Gm18:1598101; Gm18:1599717; Gm18:1599752; Gm18:1599841; Gm18:1600011;Gm18:1600033; Gm18:1600179; Gm18:1601192; Gm18:1601614; Gm18:1602244;Gm18:1603722; Gm18:1604031; Gm18:1605443; Gm18:1606442; Gm18:1606566;Gm18:1606647; Gm18:1609397; Gm18:1610935; Gm18:1612466; Gm18:1612553;Gm18:1614300; Gm18:1614960 Gm18:1618118; Gm18:1626263; Gm18:1626278;Gm18:1627202; Gm18:1627204; Gm18:1629930; Gm18:1634611; Gm18:1643225;Gm18:1653887; Gm18:1654681; Gm18:1654687; Gm18:1657025; Gm18:1680507;Gm18:1700832; Gm18:1700885; Gm18:1701854; Gm18:1702482; Gm18:1702563;Gm18:1702741; Gm18:1703321; Gm18:1706708; Gm18:1706842; Gm18:1707082;Gm18:1707115; Gm18:1707377; Gm18:1708549; Gm18:1717352; Gm18:1721829;Gm18:1723649; Gm18:1723650; Gm18:1724082; Gm18:172553; Gm18:1725630;Gm18:1725815; Gm18:1725932; Gm18:1725991; Gm18:1726068; Gm18:1727330;Gm18:1727343; Gm18:1727903; Gm18:1728146; Gm18:1728824; Gm18:1729347Gm18:1729673; Gm18:1729866; Gm18:1730855; Gm18:1731068; Gm18:1731184;Gm18:1731725; Gm18:1731938; Gm18:1734691; Gm18:1735510; Gm18:1740118;Gm18:1747766; Gm18:1751156; Gm18:1752808; Gm18:1754310; Gm18:1754895;Gm18:1759167; Gm18:1759307; Gm18:1761263; Gm18:1762686; Gm18:1763519;Gm18:1768783; Gm18:1768805; Gm18:1769619; Gm18:1773903; Gm18:1773911;Gm18:1778021; Gm18:1783028; Gm18:1783194; Gm18:1783357; Gm18:1785320;Gm18:1787549; Gm18:1789215; Gm18:1789352; Gm18:1789553; Gm18:1789934;Gm18:1805509; Gm18:1859739; Gm18:1863987; Gm18:1864738; Gm18:1877951;Gm18:1881755; Gm18:1607524; Gm18:1888247; Gm18:1845911; Gm18:1846008;Gm18:1565826; or Gm18:1918014; or a marker closely linked thereto onlinkage group G; and, b) instructions for using the primers or probesfor detecting the one or more marker loci and correlating the detectedmarker loci with predicted resistance to soybean cyst nematode.